You don’t need to add the exe of whatever mod tool to Steam, use Steam Tinker Launch. It lets you add an exe to run instead of the game, concurrent with the game, or injected after the game is up, and it will run in the same prefix that Proton uses for that game. It also has tools for installing and using several mod managers, and generally a ton of good features for tinkering with the game.

The main issue I haven’t solved is getting something like the Nexus mods “open in manager” to work. My guess is I might have to install, run, and configure a web browser inside the prefix, but that sounds really annoying so I haven’t tried it.