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Microsoft accidentally leaks internal tool that can enable hidden Windows 11 features
(www.windowscentral.com)
This is a most excellent place for technology news and articles.
Generally you use some kind of tool to manage/update the mods and set them to load in the right order. While those tools may also work under Linux with Proton/Wine/etc, each app you launch typically has its own isolated folders. So in order to get it to work, you'd need to change where that mod manager app uses to use the folders that Proton/etc configured for the actual game like Skyrim. That's compared to just installing the mod configurator/launcher app and having it start Skyrim for you on Windows.
The fact that there's a 60 page guide on how to do it tells you it's not as easy as on Windows: https://www.nexusmods.com/skyrimspecialedition/mods/91500?tab=description
Aaand I'll be using Windows for awhile I guess.
Kudos for the author putting that together.
I think the best you can do is still dual boot Linux and Windows, not ideal but at least you're avoiding most of these issues.
I might try that, just to get used to it and learn how it's structured. All I use my PC for now is gaming, music and movies. I barely even browse the Internet on it anymore.