Stardew Valley and Minecraft modder reporting in with no issues. In general, anything Steam is moddable without issues.

It would be weird for a mod to break compatibility of a game unless it’s a DLL hack

Anything that’s steam workshop should just work for the most part.

There’s also steam tinker launcher which you can use as a shim between steam and your proton in order to hook modloaders like modorganizer for Skyrim.

Anything that’s “drag and drop” should also work seamlessly.

Worst case scenario you can add your mod organizer as a non-steam game and browse to your game folder in the mod tool.

Same as far as I can tell. I installed model swap mods for several games, workshop mods for binding of isaac and terraria, and did other random things to games like tweak configs and shit. All of it worked fine. The biggest issues I had is installing random old games in my collection to my steam deck that weren’t on steam already, and even that I still managed to make it work.

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

Cyberpunk 2077 mods work great from Nexus Mods. World of Warcraft mods work great from Curseforge.

I was able to add a couple of mods that I created myself to Rimworld just fine.

For terraria tmodloader works no issue, I think forge has a native client for WoW, and Minecraft is linux native anyway EDIT: I only ever modded terraria and minecraft so idk about any more