Sorry if there's a lot of technical terms.

My anecdotal experience is that Skyrim modding under Linux worked surprisingly well. Despite that I think I would still say "YMMV". I have it running under Lutris-GE-Proton8-13.

I used the GOG release because having local access to the installer is a major win. Note that even if you don't install the AE upgrade it's the same version number, 1.6.659 so bear this in mind when installing SKSE64 and mods. I think there's a specific release of SKSE64 for GOG. Many mods label that version as AE only, which isn't true of the GOG release.

I chose to install in Lutris because of how easy it is to manipulate prefixes. I had issues with the automated scripts, which I expected. So I did it myself.

I downloaded Skyrim from GOG and installed Skyrim using the "Install a Windows game from media" option, then run once from the launcher to ensure everything was initialised before modding.

Inside this prefix I installed MO2 using "Run EXE inside WINE prefix".

I chose that mod manager because I used it on Windows and it worked just fine. I don't know a lot about Vortex. There's a DLL to add support for Epic and GOG installs of Skyrim. I duplicated the Skyrim SE runner and changed the target to ModOrganizer dot exe. There's a UI bug that makes reordering mods act weird, just click another mod entry if it gets stuck.

The Nemesis issue I had, which appears to be a Linux/WINE problem - the solution given (Extract it to the Data folder then run the executable from MO2 with VFS) worked for me.

TBH my modlist is pretty tame compared to most that I've come across so I didn't expect many problems. LOOT worked as expected so I just let LOOT handle my load order.

There's probably more to it but this is what I remember. Happy modding!

Modlist

Nemesis issue

Mod Organizer 2

Super useful tool to help manage proton versions