Is that true? In my console output I get:
[15:29:43] [main/INFO] [GradleStart]: username: MistMaestro
[15:29:43] [main/INFO] [GradleStart]: Extra: []
[15:29:43] [main/INFO] [GradleStart]: Running with arguments: [--userProperties, {}, --assetsDir, C:/Users/agilroy/.gradle/caches/minecraft/assets, --assetIndex, 1.12, --accessToken{REDACTED}, --version, 1.12.2, --username, MistMaestro, --tweakClass, net.minecraftforge.fml.common.launcher.FMLTweaker, --tweakClass, net.minecraftforge.gradle.tweakers.CoremodTweaker]
[15:29:43] [main/INFO] [LaunchWrapper]: Loading tweak class name net.minecraftforge.fml.common.launcher.FMLTweaker
[15:29:43] [main/INFO] [LaunchWrapper]: Using primary tweak class name net.minecraftforge.fml.common.launcher.FMLTweaker
[15:29:43] [main/INFO] [LaunchWrapper]: Loading tweak class name net.minecraftforge.gradle.tweakers.CoremodTweaker
[15:29:43] [main/INFO] [LaunchWrapper]: Calling tweak class net.minecraftforge.fml.common.launcher.FMLTweaker
[15:29:43] [main/INFO] [FML]: Forge Mod Loader version 14.23.4.2732 for Minecraft 1.12.2 loading
[15:29:43] [main/INFO] [FML]: Java is Java HotSpot(TM) 64-Bit Server VM, version 1.8.0_101, running on Windows 10:amd64:10.0, installed at C:\Program Files\Java\jdk1.8.0_101\jre
[15:29:43] [main/ERROR] [FML]: Apache Maven library folder was not in the format expected. Using default libraries directory.
[15:29:43] [main/ERROR] [FML]: Full: C:\Users\agilroy\.gradle\caches\modules-2\files-2.1\org.apache.maven\maven-artifact\3.5.3\7dc72b6d6d8a6dced3d294ed54c2cc3515ade9f4\maven-artifact-3.5.3.jar
[15:29:43] [main/ERROR] [FML]: Trimmed: c:/users/agilroy/.gradle/caches/modules-2/files-2.1/org.apache.maven/maven-artifact/3.5.3/
[15:29:43] [main/INFO] [FML]: Managed to load a deobfuscated Minecraft name- we are in a deobfuscated environment. Skipping runtime deobfuscation
[15:29:43] [main/INFO] [FML]: Detected deobfuscated environment, loading log configs for colored console logs.
[15:29:45] [main/INFO] [FML]: Ignoring missing certificate for coremod FMLCorePlugin (net.minecraftforge.fml.relauncher.FMLCorePlugin), we are in deobf and it's a forge core plugin
[15:29:45] [main/INFO] [FML]: Ignoring missing certificate for coremod FMLForgePlugin (net.minecraftforge.classloading.FMLForgePlugin), we are in deobf and it's a forge core plugin
[15:29:45] [main/INFO] [FML]: Searching C:\ModdingWorkspace\run\assets\.\mods for mods
[15:29:45] [main/INFO] [LaunchWrapper]: Calling tweak class net.minecraftforge.gradle.tweakers.CoremodTweaker
[15:29:45] [main/INFO] [GradleStart]: Injecting location in coremod net.minecraftforge.fml.relauncher.FMLCorePlugin
[15:29:45] [main/INFO] [GradleStart]: Injecting location in coremod net.minecraftforge.classloading.FMLForgePlugin
[15:29:45] [main/INFO] [LaunchWrapper]: Loading tweak class name net.minecraftforge.fml.common.launcher.FMLInjectionAndSortingTweaker
[15:29:45] [main/INFO] [LaunchWrapper]: Loading tweak class name net.minecraftforge.fml.common.launcher.FMLDeobfTweaker
[15:29:45] [main/INFO] [LaunchWrapper]: Loading tweak class name net.minecraftforge.gradle.tweakers.AccessTransformerTweaker
[15:29:45] [main/INFO] [LaunchWrapper]: Calling tweak class net.minecraftforge.fml.common.launcher.FMLInjectionAndSortingTweaker
[15:29:45] [main/INFO] [LaunchWrapper]: Calling tweak class net.minecraftforge.fml.common.launcher.FMLInjectionAndSortingTweaker
[15:29:45] [main/INFO] [LaunchWrapper]: Calling tweak class net.minecraftforge.fml.relauncher.CoreModManager$FMLPluginWrapper
[15:29:48] [main/ERROR] [FML]: FML appears to be missing any signature data. This is not a good thing
[15:29:48] [main/INFO] [LaunchWrapper]: Calling tweak class net.minecraftforge.fml.relauncher.CoreModManager$FMLPluginWrapper
[15:29:48] [main/INFO] [LaunchWrapper]: Calling tweak class net.minecraftforge.fml.common.launcher.FMLDeobfTweaker
[15:29:49] [main/INFO] [LaunchWrapper]: Calling tweak class net.minecraftforge.gradle.tweakers.AccessTransformerTweaker
[15:29:49] [main/INFO] [LaunchWrapper]: Loading tweak class name net.minecraftforge.fml.common.launcher.TerminalTweaker
[15:29:49] [main/INFO] [LaunchWrapper]: Calling tweak class net.minecraftforge.fml.common.launcher.TerminalTweaker
[15:29:49] [main/INFO] [LaunchWrapper]: Launching wrapped minecraft {net.minecraft.client.main.Main}
[15:29:50] [main/INFO] [minecraft/Minecraft]: Setting user: MistMaestro
[15:29:56] [main/WARN] [minecraft/GameSettings]: Skipping bad option: lastServer:
[15:29:56] [main/INFO] [minecraft/Minecraft]: LWJGL Version: 2.9.4
[15:29:57] [main/INFO] [FML]: -- System Details --
Details:
Minecraft Version: 1.12.2
Operating System: Windows 10 (amd64) version 10.0
Java Version: 1.8.0_101, Oracle Corporation
Java VM Version: Java HotSpot(TM) 64-Bit Server VM (mixed mode), Oracle Corporation
Memory: 445135024 bytes (424 MB) / 568852480 bytes (542 MB) up to 3786407936 bytes (3611 MB)
JVM Flags: 0 total;
IntCache: cache: 0, tcache: 0, allocated: 0, tallocated: 0
FML:
Loaded coremods (and transformers):
GL info: ' Vendor: 'Intel' Version: '4.5.0 - Build 23.20.16.4973' Renderer: 'Intel(R) HD Graphics 530'
[15:29:57] [main/INFO] [FML]: MinecraftForge v14.23.4.2732 Initialized
[15:29:58] [main/INFO] [FML]: Starts to replace vanilla recipe ingredients with ore ingredients.
[15:29:58] [main/INFO] [FML]: Replaced 1036 ore ingredients
[15:29:58] [main/INFO] [FML]: Searching C:\ModdingWorkspace\run\assets\.\mods for mods
[15:29:59] [main/INFO] [FML]: Forge Mod Loader has identified 5 mods to load
[15:30:00] [main/INFO] [FML]: Attempting connection with missing mods [minecraft, mcp, FML, forge, examplemod] at CLIENT
[15:30:00] [main/INFO] [FML]: Attempting connection with missing mods [minecraft, mcp, FML, forge, examplemod] at SERVER
[15:30:00] [Thread-3/INFO] [FML]: Using sync timing. 200 frames of Display.update took 78672809 nanos
[15:30:02] [main/INFO] [minecraft/SimpleReloadableResourceManager]: Reloading ResourceManager: Default, FMLFileResourcePack:Forge Mod Loader, FMLFileResourcePack:Minecraft Forge, FMLFileResourcePack:Example Mod, jabelar_resource_pack.zip
[15:30:02] [main/INFO] [FML]: Processing ObjectHolder annotations
[15:30:02] [main/INFO] [FML]: Found 1197 ObjectHolder annotations
[15:30:02] [main/INFO] [FML]: Identifying ItemStackHolder annotations
[15:30:02] [main/INFO] [FML]: Found 0 ItemStackHolder annotations
[15:30:03] [main/INFO] [FML]: Configured a dormant chunk cache size of 0
[15:30:03] [main/INFO] [STDOUT]: [com.blogspot.jabelarminecraft.examplemod.MainMod:preInit:101]: preInit() Example Mod
[15:30:03] [Forge Version Check/INFO] [forge.VersionCheck]: [forge] Starting version check at http://files.minecraftforge.net/maven/net/minecraftforge/forge/promotions_slim.json
[15:30:03] [main/INFO] [STDOUT]: [com.blogspot.jabelarminecraft.examplemod.init.ModConfig:initConfig:47]: Example Mod config path = C:\ModdingWorkspace\run\assets\config\examplemod.cfg
[15:30:03] [main/INFO] [STDOUT]: [com.blogspot.jabelarminecraft.examplemod.init.ModConfig:initConfig:48]: Config file exists = true
[15:30:03] [main/INFO] [STDOUT]: [com.blogspot.jabelarminecraft.examplemod.init.ModConfig:syncConfig:67]: Allow unrealistic deconstruction = false
[15:30:03] [main/INFO] [STDOUT]: [com.blogspot.jabelarminecraft.examplemod.init.ModConfig:syncConfig:71]: Allow horse armor crafting = true
[15:30:03] [main/INFO] [STDOUT]: [com.blogspot.jabelarminecraft.examplemod.init.ModConfig:syncConfig:76]: Allow enchanted book deconstruction = true
[15:30:03] [main/INFO] [STDOUT]: [com.blogspot.jabelarminecraft.examplemod.init.ModConfig:syncConfig:81]: Allow partial deconstruction = true
[15:30:03] [main/INFO] [STDOUT]: [com.blogspot.jabelarminecraft.examplemod.init.ModTileEntities:registerTileEntities:30]: Registering tile entities
[15:30:03] [main/INFO] [STDOUT]: [com.blogspot.jabelarminecraft.examplemod.init.ModFluids:registerFluids:54]: Registering fluids
[15:30:03] [main/INFO] [STDOUT]: [com.blogspot.jabelarminecraft.examplemod.init.ModFluids:registerFluids:63]: Registering fluid: slime with bucket = true
[15:30:03] [main/INFO] [STDOUT]: [com.blogspot.jabelarminecraft.examplemod.init.ModNetworking:registerSimpleNetworking:42]: Registering simple networking
[15:30:03] [main/INFO] [STDOUT]: [com.blogspot.jabelarminecraft.examplemod.init.ModWorldGen:findFreeDimensionID:56]: Found free dimension ID = 2
[15:30:03] [main/INFO] [STDOUT]: [com.blogspot.jabelarminecraft.examplemod.worldgen.WorldTypeCloud:<init>:44]: Constructing WorldTypeCloud
[15:30:03] [main/INFO] [STDOUT]: [com.blogspot.jabelarminecraft.examplemod.proxy.ClientProxy:preInit:144]: on Client side
[15:30:03] [main/INFO] [STDOUT]: [com.blogspot.jabelarminecraft.examplemod.proxy.ClientProxy$MouseHelperAI:<init>:462]: Constructing MouseHelper for AI bots
[15:30:03] [Forge Version Check/INFO] [forge.VersionCheck]: [forge] Found status: OUTDATED Target: 14.23.4.2739
[15:30:03] [main/INFO] [STDOUT]: [com.blogspot.jabelarminecraft.examplemod.proxy.ClientProxy:fixLocaleClass:163]: Swapping in custom locale class
[15:30:03] [Forge Version Check/INFO] [forge.VersionCheck]: [examplemod] Starting version check at https://raw.githubusercontent.com/jabelar/ExampleMod-1.12/master/src/main/resources/versionChecker.json
[15:30:03] [main/INFO] [STDOUT]: [com.blogspot.jabelarminecraft.examplemod.init.ModBlocks$RegistrationHandler:onEvent:107]: Registering Blocks
[15:30:03] [main/INFO] [STDOUT]: [com.blogspot.jabelarminecraft.examplemod.blocks.BlockCompactor:<init>:61]: Constructing BlockCompactor instance
[15:30:03] [main/INFO] [STDOUT]: [com.blogspot.jabelarminecraft.examplemod.blocks.BlockCloud:<init>:47]: BlockCloud constructor
[15:30:03] [main/INFO] [STDOUT]: [com.blogspot.jabelarminecraft.examplemod.blocks.BlockCloudBedrock:<init>:42]: BlockCloud constructor
[15:30:03] [main/INFO] [STDOUT]: [com.blogspot.jabelarminecraft.examplemod.blocks.BlockParticleEmitter:<init>:47]: BlockParticleEmitter constructor
[15:30:03] [main/INFO] [FML]: Applying holder lookups
[15:30:03] [main/INFO] [FML]: Holder lookups applied
[15:30:03] [main/INFO] [STDOUT]: [com.blogspot.jabelarminecraft.examplemod.init.ModItems$RegistrationHandler:onEvent:74]: Registering items
[15:30:03] [main/INFO] [STDOUT]: [com.blogspot.jabelarminecraft.examplemod.init.ModBlocks$RegistrationHandler:registerItemBlocks:132]: Registering ItemBlocks
[15:30:03] [main/INFO] [FML]: Applying holder lookups
[15:30:03] [main/INFO] [FML]: Holder lookups applied
[15:30:03] [main/INFO] [STDOUT]: [com.blogspot.jabelarminecraft.examplemod.init.ModBiomes$RegistrationHandler:onEvent:52]: Registering biomes
[15:30:03] [main/INFO] [STDOUT]: [com.blogspot.jabelarminecraft.examplemod.init.ModEnchantments$RegistrationHandler:onEvent:46]: Registering Enchantments
[15:30:03] [main/INFO] [STDOUT]: [com.blogspot.jabelarminecraft.examplemod.init.ModEntities$RegistrationHandler:onEvent:63]: Registering entities
[15:30:03] [main/INFO] [STDOUT]: [com.blogspot.jabelarminecraft.examplemod.init.ModPotions$RegistrationHandler:onEvent:65]: Registering potions
[15:30:03] [main/INFO] [STDOUT]: [com.blogspot.jabelarminecraft.examplemod.init.ModPotions$RegistrationHandler:onTypeEvent:86]: Registering potion types
[15:30:03] [main/INFO] [STDOUT]: [com.blogspot.jabelarminecraft.examplemod.init.ModSounds$RegistrationHandler:onEvent:80]: Registering sound events
[15:30:03] [main/INFO] [STDOUT]: [com.blogspot.jabelarminecraft.examplemod.init.ModProfessions$RegistrationHandler:onEvent:63]: Registering villager professions
[15:30:03] [main/INFO] [FML]: Applying holder lookups
[15:30:03] [main/INFO] [FML]: Holder lookups applied
[15:30:03] [main/INFO] [STDOUT]: [com.blogspot.jabelarminecraft.examplemod.init.ModItems$RegistrationHandler:onModelEvent:94]: Registering item models
[15:30:03] [main/INFO] [STDOUT]: [com.blogspot.jabelarminecraft.examplemod.init.ModItems$RegistrationHandler:onModelEvent:109]: Registering custom item models
[15:30:03] [main/INFO] [STDOUT]: [com.blogspot.jabelarminecraft.examplemod.init.ModBlocks$RegistrationHandler:onModelEvent:170]: Registering block models
[15:30:03] [main/INFO] [FML]: Applying holder lookups
[15:30:03] [main/INFO] [FML]: Holder lookups applied
[15:30:03] [main/INFO] [FML]: Injecting itemstacks
[15:30:03] [main/INFO] [FML]: Itemstack injection complete
[15:30:05] [Forge Version Check/INFO] [forge.VersionCheck]: [examplemod] Found status: UP_TO_DATE Target: null
[15:30:08] [Sound Library Loader/INFO] [minecraft/SoundManager]: Starting up SoundSystem...
[15:30:09] [Thread-5/INFO] [minecraft/SoundManager]: Initializing LWJGL OpenAL
[15:30:09] [Thread-5/INFO] [minecraft/SoundManager]: (The LWJGL binding of OpenAL. For more information, see http://www.lwjgl.org)
[15:30:09] [Thread-5/INFO] [minecraft/SoundManager]: OpenAL initialized.
[15:30:09] [Sound Library Loader/INFO] [minecraft/SoundManager]: Sound engine started
[15:30:17] [main/INFO] [FML]: Max texture size: 16384
[15:30:17] [main/INFO] [minecraft/TextureMap]: Created: 512x512 textures-atlas
[15:30:18] [main/INFO] [STDOUT]: [com.blogspot.jabelarminecraft.examplemod.client.models.ModelSlimeBag:bake:143]: Baking custom model
[15:30:18] [main/INFO] [STDOUT]: [com.blogspot.jabelarminecraft.examplemod.init.ModItems$RegistrationHandler:onModelEvent:125]: Models have been baked
[15:30:19] [main/INFO] [STDOUT]: [com.blogspot.jabelarminecraft.examplemod.init.ModRecipes$RegistrationHandler:onEvent:42]: Registering recipes
[15:30:19] [main/INFO] [FML]: Applying holder lookups
[15:30:19] [main/INFO] [FML]: Holder lookups applied
[15:30:19] [main/INFO] [STDOUT]: [com.blogspot.jabelarminecraft.examplemod.MainMod:init:129]: init()
Basically, I see it start pre-init, then do block registration (and objectholder injection), then item registration (and objectholder injection), then other registrations (like biomes) (and objectholder injection), then init. It seems that all the registration happens between pre-init and init.