Since Nexus Mod Manager for Linux fizzled out, I was excited to find a decent mod manager. It has built-in support for about 100 games, but adding other games seems pretty easy. I pasted in the Steam ID and path the the .exe of a proton game (MineMogul), and then everything just worked.
I have had great luck with amethyst so far, including large collections installed to cyberpunk 2077.