

I haven’t tested this, but fairly sure you could just install vortex, mo2 or whatever other modmanager to same prefix as where the game is.
Yeah, you can use protontricks to execute any executable inside the WINE environment. You can take the command used to do that and put it in a .desktop file so you can run the program from a desktop icon or launcher.
Installing mods mostly considered a ‘problem’ by the standard of gaming on Steam where you just press play and let Proton take the wheel. If you were running games through WINE prior to Proton, it is much easier now.

You gain the loss of the ability to play League of Legends and Fortnite