Per default controllers VR operate in keyboard/mouse mode, which may override gamepads. You can switch them to gamepad on the VR controller page of the vorpX menu. That way the won’t interfere with native gamepad handling.
However, for some games they have to work in kb/mouse mode. Whenever a game does not allow mouse and gamepad input at the same time (quite a few games work that way) and you want mouse emulated head tracking, vorpX can utilize it’s built in gamepad to mouse/kb wrapper to resolve the conflict.