"Use gamepad" isn't showing up. If the game used DirectInput I could use DevReorder to hide it, but it looks like unity doesn't use that (and sadly it wouldn't work on Linux). Unfortuantely, disabling vJoy is worse than just needing it with other games - given the way it works, it requires a full system restart when the configuration changes.
In case you want to add a temporary workaround, here's the error:
Could not create a device for 'Shaul Eizikovich vJoy - Virtual Joystick (HID)' (exception: System.NotImplementedException: The method or operation is not implemented.