Why do mods feel "a lot more problematic in BG3 so far"? More problematic than what?
I don't want to hijack the OP's thread, but yours is a valid question, politely asked, so here's my reason for having this opinion...
It was more challenging for me than Skyrim, Dragon's Dogma, and Solasta anyway. Neither Vortex nor BG3MM worked for me without me delving into the modlist file and manually changing things -- something I never had to do with those games. Even with Conan Exiles, while I often had to edit the modlist files for my servers, there was still an in-game resource that could do it for you, and the output was more approachable too (plaintext vs XML). Considering my BG3 install was about as typical as you could get (Steam library on C: & default install path), it seemed odd to run into so many difficulties even after reading and following instructions.
The other issue is, the consequences of mod failure in BG3 feel more severe vs other games requiring a similar time investment for even simple mods. In Conan Exiles, if I remove a storage mod, the chests, etc. may go away, but the data for their contents is still in the save file should I reinstall it later, and the save will still run without it.
Since it's not uncommon for mod authors to discontinue support after they get tired of a game, or for mods to stop working after a patch, I wanted to test how gracefully BG3 would handle the removal of a comparable mod (Bags, Bags, Bags for example). My suspicion/hope was that the auto-sort behavior logic would be lost and the bags would revert to normal pouches or backpacks. NOPE! Instead the save file wouldn't even load anymore. So yes, while it's always a bad idea to remove mods, there are times outside of a user's control where they might need to do so (discontinuation, etc), so the inability to fail gracefully, is a major red-flag for me.
Given my user experience and testing of scenarios I've often encountered in other games, the risk vs reward calculation is too skewed towards the side of risk for me to feel comfortable with for myself, let alone recommending to others.
This mostly boils down to you asking things of mods which they weren't made for, i.e. multiplay. If a mod works then it does not need support. More or less all the ~24 mods I use (some from EA) have been updated after patches and are still being updated.
As for Bags, Bags, Bags - were all the bags empty before you uninstalled the mod? Why would they revert as they are added by the mod not converted from something already in the game. You could also put that at Larian's door as what gets baked into a save is their responsibility.
I have only been using Bags mod since I started this run but I'm not overly impressed with it. I've seen merchants with multiple copies of the bags (the big bag which contains the other bags) and I've noticed that it sometimes sucks potions into the potions pouch on its own. Annoying in the middle of a fight when you hit the hotbar for a health potion and there are none there. Unless it gets a major update it will be gone after this game.