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
this post was submitted on 12 Jun 2023
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I've been using SteamTinkerLauncher for ages with SSE and it works great. Allowing me to use MO2 seemless tbh, even Vortex works fine.
I've played MO2 Skyrim through a Steam Link before, and for that to work you have to add MO2 with the launch options from the shortcuts you can make from MO2, this way Steam registers MO2 as a game.
I'd imagine you would need to do the same for proton to work, though that assumes it even runs.
I'm curious, is SKSE even supported through proton? Not sure why it wouldn't but still curious.