For most games I’m sure you can find a way to do it. If you use protontricks you are able to run an exe under a proton prefix for a game (basically a virtual windows drive in a folder for the game) which I’ve had pretty decent luck with.
If you play games that support mod organizer 2, there is a sh install script somewhere for support in proton/steam that works well (I can find if you like), but the program does run pretty slow and is fairly buggy. Usable with patience. Upside is it can run MO2 for a given game direct from steam if configured correctly