I agree with many of the design philosophies listed here. I am definitely more interested in making the facial/body features more pronounced (e.g. new tails, ears, horns, teeth, etc. for girls) than clothes.
Once issue I do fear running into is for some animations, namely large monster animations such as salamander_woman_1 or minotaur_woman_1, the atlas seems to be capped out at 2048 x 2048, with it being entirely filled up almost. If I were to expand upon the base girl atlas for new races, some of these atlases may need to be expanded further past 2048, which I'm not 100% sure how well spine supports since I've never really gone past that before. Perhaps further compression or reducing resolution, but I'm not sure about that. I do see some atlases such as "sactx-0-4096x4096-Crunch-StandingImage-78529d7f" under atlas_assets_all, which go as far as 4096x4096, but those aren't animated textures. Another obvious concern would be performance on lower-end machines, which you've sought to address already it seems.
Phantasy Overhaul sounds like a great name! Will be down to collaborate.
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These are some great ideas. Rooms will likely be a secondary priority, though, and will be need to be for the very end, since each room needs to have custom animations for each character type. And if new races are added, it will be a pain to have to go back in and modify the same room animations to include them. Easier to do it all in one final swoop if the project goes that far.