At the moment, when a mod wants to offer options to the user, it has to set those in the config files, or create a custom gui to allow them to set in game.
My Suggestion is to put a new "Options..." button under the "Mods..." screen on the main menu, that allows mod creators to provide an options screen in that location. Similar, a "Mods Options..." can be added to the default minecraft options screen, to allow in-game editing of those settings that are safe to do so.
It is up to the mod developers to properly respond to any changes to the options where applicable.
Note that I consider Block ID assignment explicitly outside the scope of this Suggestion. (as that should not be changed during a game.)