This might not be exactly what you are after but Enderal: Forgotten Stories, an incredible total conversion for Skyrim that in my opinion easily surpasses Skyrim in quality, is available on Steam and works out of the box.

I briefly tested Jackify, and it seems to be a great tool. I'm not able to fully test it because I don't have Nexus Mods subscription. But, I was able to test it with my old Nordic Souls files.

Guide to modding Skyrim on Linux by using a modlist:

1. You need Nexus Mods subscription to download modlists.
2. You most likely want to have Anniversary Edition of Skyrim, otherwise modding will be challenging because many mods requires it.
3. Launch Skyrim normally, and if you have Anniversary Edition, let it download all Creation Club Content (CC Content). Do not Alt-Tab out of Skyrim, or it will interrupt the download. The game will claim it downloaded everything, but you'll miss some of the CC Content. If you get any errors about files that have the letters "CC" in them, this is your problem.
4. Once the CC Content is downloaded, close Skyrim.
5. Head over to Jackify Releases. Download the latest Jackify.AppImage.
6. You might need to give it executable permission. You can typically do this by pressing the second mouse button over the icon, go to Properties -> Permissions and look for the option that says executable. Or use chmod +x /path/to/Jackify.AppImage.
7. Place Jackify.AppImage where ever you want to and launch it.
8. Go to Modlist Tasks -> Install a Modlist.
9. Select Skyrim as the game, and pick one of the Modlists. If you are out of ideas, and you have a decent computer, try Nordic Souls. Note, that you cannot combine modlists, but you can install more mods if you want to.
10. Change install and download directories, so that they have the name of the modlist in them (create new folders, for example).
11. Under the Nexus API field, there is a link. Click it, scroll to the bottom to Personal API Key section, hit the Request API Key button and copy-paste it to the API Key field. You might want to read the warning on the Nexus site, and decide yourself if you want to trust Jackify. Jackify team is planning to implement a better way to do this, but it is what it is for now.
12. Click Start Installation button, go brew some coffee, make a dinner, wash your clothes and come back to see if the installation is finished.

Once the installation is complete, Jackify adds the modlist to your Steam Library and configures the proton prefix. Make sure you are using Jackify 1.6.2 or newer, or the prefix configuration will likely fail. When you start the modlist, it will launch ModOrganizer2. Hit the big Play button to launch the game.

Nordic Souls defaults to ENB for its graphic improvements. On my old Nordic Souls, it doesn't seem to start, or it takes a very long time. Nordic Souls also comes with Community Shaders, which does the same thing. In the latest Nordic Souls version, there is a separate profile for ENB and CS. Change it from top left corner of MO2.

If you get "too many open files" error during modlist installation, you need to edit /etc/security/limits.conf and add this line to it: your_username hard nofile 524288 and then relogin, or restart.

Once you start a new save file, avoid changing the mod and plugin load orders (left and right side lists) in MO2. Doing so might break your save file, and fixing it will be difficult, because you probably won't remember the old order. Also, never uninstall or upgrade a mod, unless you are sure doing so is safe. This too can break your save file. Re-installing a mod once something has broken might not fix it.

You can install more mods using MO2. Always read the instructions given by the mod author, and follow them to a T. Pay attention to things like dependencies, incompatible mods, load orders. If the mod author doesn't mention which of the two load orders they mean, it's most likely the mod load order (left side).

If a mod comes with different versions for AE and SE (Anniversary Edition, Special Edition), you most likely need AE version of it, if you are using AE. Otherwise, SE and AE are the same, and both should work for AE.

Some modlists, such as Nordic Souls, will downgrade the Skyrim version to something like v.1.5.97. If a mod has versions for different versions of Skyrim, pay attention to this. Check the Skyrim version from the main menu of Skyrim.

This may not entirely help you if you don't have a Windows drive (I dual boot when needed, especially for modding my games easily on Windows and then moving the files over to Linux after testing it works in Windows) but:

• Log into Windoze
• Install your game if it isn't (Quick Tip: If you do have Windows and Linux on separate drives, you don't have to download the entire game again. Drag the game over to the correct folders you would have on Windows, then go to download the game. It will see the files and fetch anything you still need)
• Run the game at least once to make sure your files are created and whatnot (SkyrimPrefs.ini or whatever it is called)
• once at the main menu, download any of the anniversary edition stuff if you have them
• Use Nexus Mods modding tool Vortex and use a Collection (NOTE: If you do not have a Premium account, you can use any other program like Mod Organizer 2 or whatever if you want, I have only ever used Vortex, sorry. :/ )
• Let the mod managers do their thing
• Once all the mods from the Collection/s are installed, start the game on Windows and make sure you can get in game at least (Not all mods/Collections are created equally!)
• Log back into Linux and use your preferred File Manager program to go into your Windows drive (Mine is called basic something, I'm away from my computer right now) and move the whole game folder over to your proper Linux folder for your Steam games
• Test
• Hopefully profit?

Go to a local PC repair shop? Will be much safer than giving someone on the Internet access to your PC. Like probably 95% nothing awful happens (esp picking some random Lemmy person) but in that 5% they will drop a keylogger, get your banking login and clean you out.

Currently trying to mod Skyrim on Linux myself. I’ve got it to work now but it was a pain. I’m using MO2, it was really janky for a bit and still acts up a lot. I’m at the point now of always having MO2 open even if I’m not playing Skyrim, because closing and reopening it causes issues for me. Have you had any luck since posting this? I’m in the same boat as you, just a couple steps ahead, so I might be able to help out a little.