LIMO would absolutely work to mod Skyrim from Linux.

It is universal, it will work with anything, you just may have to do a teensy bit more manualy configuration than some game specific mod tool.

It's basically MO2, but linux native.

I've been using it for almost 2 years now, because I got tired of waiting for NexusMods to figure out how to make their own linux compatible modnmanager, and got very tired of having to do a custom MO2 install/container/whatever for every different game.

I've got my own 100+ mod sets working for Fallout New Vegas and CyberPunk 2077, via LIMO... on a Deck, on Bazzite.

LIMO supports FOMOD bundled mods, as well as more standard archives of files.

All you really have to do is construct a deployer, which is basically a pathway to the actual game directory, and then also set aside a directory for LIMO managed mods to live in.

It then does a virtual file structure that can be deployed/undeployed to/from the actual game directory, at whim.

You can manage load orders, it has mod/file conflict indicators, you can tag and group various kinds of mods by doing regex filters, you can have different mod profiles, one very neat thing it does is an automatic attempt at directory matching, ie, if somebody made a mod that didn't properly replicate the game's dir structure, it'll indicate that and allow you to tweak it a bit... don't think there is a super simple UI way to export and then share a modlist/profile yet, but presumably they just live in the var/apps/flatpak/whatever dir, somewhere.

... the only problems you may run into are things that:

Fully overwrite the actual game exe, like NVSE, but this can be worked around by maybe setting up a new profile for however you are launching the game, to point at that exe, or just manually going in and renaming the old exe to .exe.OLD or something like that, and then naming your mod exe to the same name as the original game exe, and turning off any auto updates.

You've well described a decent solution for handling SKSE, so good work!

Also problematic are things like... massive archive rectifiers, that are actually just exes or batch files or whatever, that go through and make a ton of edits to core game archive files.

Because these archive type files are basically compressed in their own way, you can't just point by point overwrite them with minor loose files, you have to make the corrections and then basically recompress them, thats what these rectifier exes and batch files do.

Generally speaking, you can just run these rectifiers through the same proton config that you use successfully for the game itself, though you may have to use ProtonTricks to add in extra dependencies like vcrun20xx or whatever, also it can be worth it to throw in some stuff to help render fonts properly with the right antialiasing.

Just make sure you've put them in the equivalently correct dir in the game as you would for following windows based instructions for using them.

Any mod that ends up, in the course of being run with the game, actually creates/writes new files beyond what is just directly installed by LIMO.

When you undeploy mods via LIMO... well, LIMO doesn't know that some advanced scripting mod writes its own config and ini files on the game executing with the mod for the first time, it doesn't know those exist, so it doesn't remove them.

For that, you again just kinda have to manually either just go in and remove them from the game dir, or, you could run those kinds of mods initially, then go into that directory where LIMO stores uncompressed mods, and add those files manually in there.

That way LIMO knows they exist, and deploys them with the mod, so your mod sees that those files already exist and thus isn't trying to do what it thinks is an initial setup every time, potentially causing lots of silly shenanigans.

I've not heard of WinBoat... What I do is just use ProtonTricks to manage the Steam compat data/prefix data for the game I am modding, and if any mod needs some kind of Windows dependency to work properly, ProtonTricks can handle installing and managing that, albeit through a somewhat clumsy UI, it is at least less tedious than manually looking up Steam's compat data/prefix locations that are all done by game id.

Just add in your dependency for that mod, to that game's compat/Proton prefix.

Hah, if you think that's bad, try fucking figuring out which steam workshop mod is which, they're also all done by workshop mod ids for the folder names, so its fucking opaque... i think there are some websites that have searchable ways of solving that problem tho.