Agreed, and one particular example I can think of is Terraria’s Steam Workshop tools. If I try and publish a texture pack using the Linux-native version of the game, it crashes, but when I use the Windows version of the game via Proton, it works just fine. Not sure if the developers have gotten around to fixing this yet.
Edit: Now that I think of it, it’s a similar story with Half-Life 2 now that they added Steam Workshop support for its 20th anniversary. Crashes on native, works fine under Proton.
I can only speak for myself here, but you could give Limo a try. It’s Linux-native (so you don’t have to run it through Wine, unlike Vortex & Mod Organizer 2), the UI works well enough for my needs, and it has Nexus Mods support (you just give it an API key in the settings, so it can download mods for you). You’ll want to read the documentation for it though, to understand what “Data” and “Bin” mean when installing mods, deployment methods, LOOT integration, etc.