Chuck, I'm fairly sure you're just going to keep running into this. My survival world hasn't had a single village successfully generate for four months now. Honestly, I don't think anyone is trying to fix this.
If moss gets a net gain of bonemeal, I have no idea why nylium can't. Nylium-based bonemeal farms are relog-proof (unlike the moss farms), satisfying to build and use, and were one of my favorite 1.16-1.17 features.
Saturation is definitely still broken. I just installed a bunch of brown mooshrooms all over my base, fed them blue orchids, and found that the resulting suspicious stew behaves identically to mushroom stew.