I don't seem to have issues modding games like Skyrim, Fallout 4 or Factorio on Linux
it's a question of tooling, modding kits
most times it this tooling which causes issues not the mod itself
For very popular games it's not rare if moddingkit/tooling producer (or contributes) made the tooling work on Linux, but it can be very hit or miss.
but it increasingly more "just works", kinda, somewhat
Do you use executable mods? Downgraders, engine fixes, etc? I'm also curious what mod manager you use, because getting MO2 to work under linux is a bit janky as well.