I have not done mods in a while, but I could have sworn it was as easy as adding it to Steam too, and it detected the game in its "wine" directory. Or something like that? I'm not too sure...
The most notable example is probably Wabbajack, a tool that manages modpacks for many games but is best known for TES games, where modlists consist of hundreds of mods and are a pain to manually install. Ironically it is a WPF app written in modern C#, so in principle _could_ run under Wine just fine, and could even be ported to a native GUI app via Avalonia UI or similar.
Unfortunately, it is apparently quite fragile in its path management and relies on both Edge WebView to download mods and Windows Steam to install them, so the maintainers think it's not viable to make it run under Wine [0], although of course someone has bashed together a script to work around it [1]. That last one is quite recent so I just discovered it while writing this post!
[0] https://github.com/wabbajack-tools/wabbajack/issues/2521
[1] https://github.com/Omni-guides/Wabbajack-Modlist-Linux/blob/...