https://github.com/rockerbacon/modorganizer2-linux-installer
Small caveat at the moment though is that Protontricks is borked and requires a more up to date version than what's on most repos and flathub. I used the pipx install for Protontricks and that one worked though, but I think the beta branch on Flathub has an updated version now as well, which hopefully goes stable soon.
Nexus is also working on a new cross platform compatible mod manager now, but that's going to be far away.
For a lot of other games r2modman + Thunderstore are also working natively on Linux. Games like Stardew Valley have a native mod manager like Stardrop.
Yes. It's so garbage I wrote a master's thesis on how shit it is. If I didn't have over 1,000 hours in the game, it would have been substantially harder to do this.