Just spitballing, but most of modding skyrim is just loading .esm and .esp files in the right order.

You may be able to get the modlist downloaded, load order sorted (and any merged patches made if those are still a thing) in a Windows VM, then shift the files and load order list over to Linux so you're just struggling with Linux compatibility to run instead of also with the setup of the mods.

As far as I know, that's the reccomended way to handle modding for a lot of games running on linux through compat layer stuff.

As far as mods themselves, I'd pick one of the more popular packs on nexus or wabbajack that appeals to you and doesn't seem to have a lot of complaints about bugs in the comments.

Modding has multiple hurdles. Getting the tools set up, getting the game set up, selecting and installing the mods, working out compatibility issues, and making sure everything runs at the end. By sticking with a popular modpack, you cut out selecting the mods and having to figure out getting them working together yourself. By using a Windows VM for initial setup, you cut out most of the struggles of getting the tools working on Linux. Hopefully that would cut the challenges down to a managable level.