Hah, yes I think I confused myself. What I meant to say was add the emulator as a non-steam game, and launch it that way (via Steam) to configure the controllers in the emulator's settings. Reason being is that Steam creates "virtual" xinput devices and I've noticed it can confuse some emulators if you configure everything without Steam running (if it's a dinput device for example). For more complicated configurations yes you'll need to make a "Cemu" (for example) setting and manually load it on a per-game basis.
Love this plugin, by the way. Looking forward to the BigBox fix!