My input isn’t going to be very useful but as a point of data, I’ve never had trouble with my 8bitdo controllers and Linux.
Sometimes they don’t pair right away on the Switch, but Linux has been fine.
Now I’m trying to remember which controller I used to test Yuzu…
Weird as it is, I’ve heard launching games through Steam Big Picture mode with the controller connected can help but that might just be more a key mapping thing than anything else.