the problem is that if you run plutonium you don't have steams built in controller emulator cuz plutonium doesnt use steam. the easiest and most brilliant way to fix this is to add plutonium.exe as a non steam game. then you will have steams built in controller emulator as well as a modded client. even i impressed myself when i thought of all of this. this will get your controller working. im using a dualshock 4 rn.
and just as a side note, for future endeavors, you can do this with lots of things that need a controller emulator. for example you can add ubisoft games to your steam to take advantage of the steam controller emulator on ubisoft games.