MO2 works fine on Linux! It’s a bit slow to start but I found it very usable, a bit less polished than Vortex maybe but it absolutely gets the job done and I got my head around it inside of an hour.
How did you install it? Maybe with a different method it would work for me better (even though now I'll probably just stick with my own tool I'm still curious)
https://github.com/Furglitch/modorganizer2-linux-installer
Download, run install.sh, follow the instructions given. It replaces the game effectively in Steam, which does mean you have to launch MO2 anytime you want to play the game, but I found that at worst, slightly annoying.