I'm having the same issue as OP, but I can't see anything within my load order that this document doesn't suggest. I rolled back to patch 6, deleted all my mods, re-installed BG3MM, re-installed the mods, made sure to clear out both local files and steamapp files, and re-downloaded Script Extender.
I'm unsure which version of Script Extender I should have - I've tried the pre-patch 7 version and the latest version and it doesn't seem to make a difference. The override mods I have are the latest pre-patch 7 versions of ImprovedUI (3.21.0.0), ModFixer (0.0.0.0), and Trips Shader (2.1.0.0).
The only non-visual mods I have are Party Limit Begone, Rogues Extra, Unique Tav, and RemoveMultiplayerCharacter (I think this is Recruit Any NPC).
When I try to export my load order in BG3MM (I have v1.0.10.0 since I read the latest version is incompatible with the patch 6 rollback), it gives me this pop-up:
When I launch the game and try to open a save, it basically lists every single mod and says that they've been disabled and launching the save without them enabled could cause problems. When I exit the game and re-open BG3MM they've all been shunted over to the inactive side.
I basically rolled back to patch 6 because a bunch of mods I wanted to use on a new patch 7 save weren't compatible. Now none of my mods are working and I can't figure out why! Load order is below - I didn't have any of these issues after patch 7 except for figuring out which mods I should just make inactive since they clashed with patch 7. I'm so over this!!