Years ago I tried modding Fallout New Vegas and I think 4 on Fedora ages (I was running Fedora 28 at the time) ago using Mod Organizer 2 and it wouldn’t work for reasons I didn’t understand, possibly file system related. I’m thinking of switching to Pop! OS full time but I’d still like to play either modded Skyrim or FO4 from time to time, preferably using MO2.
So I use MO2 for Fallout 4 on my Steam Deck.
Initial setup is a pain in the ass, but it’s worth it. Installing MO2 with Wine is easy, getting nxm links to work using scripts and .desktop files was not.
Also making sure that you have the right compatibility utility going is also super important, I know for FO4 I had to run a super specific version of Proton-GE.
I’d say jumping through those hoops is worth it tho, I get to play FO4 just how I like all from the comfort of my bed, and getting your favorite games to work in an operating system you actually like is sublime~