I never got Skyrim with mods running through wine or proton, never found a good way to untangle the mess of Steam, Skyrim, Mod Organiser 2.
That's why Skyrim is one of the last games running in dual boot Windows
this post was submitted on 12 Jun 2023
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I'm not sure completely so someone will have to chime in with the specifics but I remember watching a streamer that played modded on Linux and I'm pretty sure that he ran mo2 through steam for the proton compatibility so that when he launched skse in mo2 it would launch under proton.
I personally use MO2 to mod my Skyrim. This script makes getting it setup very easy. MO2 launches every time you press "Play" on Steam. https://github.com/rockerbacon/modorganizer2-linux-installer
I've been using SteamTinkerLauncher for ages with SSE and it works great. Allowing me to use MO2 seemless tbh, even Vortex works fine.