Did you ever resolve this? Both Sudachi and Eden have this exact same problem. I will get the controls working independently in the config menu despite both of them using Xbox One Controller 0 - but as soon as I try to set ANYTHING up in an actual game, Player One will control both inputs. Every. Single. Time. I have tried enabling and disabling settings in the config file. I can't get this thing working.
I have wiped my config folder as well. I cannot get this thing to work. Using an Xbox One (model 2) wireless adapter AND Bluetooth. Windows 10. One is a Series X, the other is Series S.