Shmacky-McNuts: The problem people are talking about is actually SkyUI running through MO2 and dropping some odd menu options, though it mostly functions. Still grabbing all the requirements, so I do not really know what to expect.
I'd have to have see the specifics, but SKSE mods without their SKSE libraries can do that, similar to how iNeed wasn't working without its libraries.
RaceMenu is a good example. RaceMenu "works" for all things Skyrim already had, but things like body sliders, overlays, and face modeling are completely absent. (Still better than Skyrim's own character creator.)
Some mods also use SKSE for their mod configuration settings management, thus those areas are also nonfunctional.
Shmacky-McNuts: One more thing, does MO2 have symlinks? Still new to MO2 and while I do not have the steam version. I was not sure if this would copy and paste the Profiles text stuff over to the APP/Local folder. Gets annoying trying to juggle that too. Plus having to test by turning the game on to repopulat the text file.....guhh......arduous. I mean I know when it works, its fine. But man, it is tedious for like 100 mods.
MO2 uses a virtual file system. It's why you can "see" all the mods in its virtual file explorer, but in windows explorer, they aren't actually there. It'll use what's on your physical file system if something's there. That's why copy-pasting works. Because MO2 isn't putting the files in its virtual filesystem where Skyrim is expecting, we have to do it for it until they fix it.
If you have admin access, I do recommend looking up how to symlink them (using the mklink command from the command console) until they get it fixed. The SKSE directory is a different beast; you could symlink the details, but that copy-paste dance should happen much less often enough that I don't think it's really worth it.
Vortex, however, apparently uses links (hard or symbolic, depending on what's available). Not sure what it does on a file system that doesn't support links. Copy-paste, I guess.