If you want, I looked up a step-by-step Youtube tutorial on how to set up Mod Organizer on Linux after I saw your post. Here's the link: https://youtu.be/OEbZ3hNcoRg
Also, top comment mentions that the process is different if Steam and Proton Tricks are installed as Flatpaks. Apparently you'll then need to give them permission to access the MO2 folder.
Hope this helps, sorry I can't do more at the moment