I want to say those are common issues that many of us face with MO2. I can at least say that everything works fine for me also with the exception of what you have outlined. From what I've also noticed, others have had to rely on 'workarounds' as well (i.e. Mod Organizer 2 SSE Sync Plugins Batch) to bypass these quirks. Given that MO2 is in beta phase at this time, if the development proceeds then these should get sorted out one way or another. You may want to follow the issues list over at GitHub. I've found one two related to what you wrote about: 2.0.8.1 Plug in list not being remembered when external tools are used #30 Local Game Settings and Savegames are not working #17
I found that I was able to perform a workaround by toggling "preferred" for the FOMOD installer plugin when it comes to certain mods that have this issue. The NCC based install plugin seems to work just fine for those. It's a hassle switching back and forth if you've got it happening on many mods, so yeah, I suppose downgrading MO might be the better option in those cases.
Great tip! Another thing that might be possible, is to set the INI files for the SLRE profile to 'read-only' within Windows Explorer, once you've got it configured the way you like.
Quick question, somewhat related (apologies in advance if someone that I'm hijacking the thread)... does MO's built-in LOOT support userlists? If so, does it read from the %APPDATA% folder just as the standalone version of LOOT does? I ask because I'm using AOS as well, so I'm wondering if sorting within MO ignores my userlist.