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.