I like the sound of parallel loading, but I seriously doubt that textures can be stitched in parallel, but if that's been parallelized, good work, i'm impressed.
One thing I'm not sure of is this statement "I don't feel like periodically cleaning my disk of cached texture atlases, especially since different packs with the same mods would cause a new atlas set to be cached, and a resource pack change would cause a re-cache, and pack devs would see their test installation bloat with every mod added to the pack."
Let's think of set theory. We have set M. set M contains all mods in your mod pack. any mod 'm' is a set containing three items: 1: s, the space that the mod takes up. 2: a set C containing source files for the mod. 3: a set R, which contains all of the resources that a mod uses. Similarly, we have an Atlas set A, for which there is one A for every one M. Set A contains all R sets within M, as well as a D set, for Directory. The A set also contains a unique element s, which is the space that A takes up.
Then it follows that so long as set C is lesser in space than set D, then Mc will take up less space than Ac. In short, The atlas will always take up less space than the mods, considering that most worlds are bigger than the mods, then space won't be an issue, especially if you cull old atlases automatically.