Hi @FairweatherIT - just jumping in with some clarifications 
I just checked the source code, and it seems that support for using the Navigator’s pins as relay outputs was only added in the latest stable (4.4.0). I’ve added that to the guide note.
ArduRover doesn’t use the same type of joystick control as ArduSub, so instead of using the autopilot’s internally registered button functions (via the MANUAL_CONTROL MAVLink message) it’s necessary to send DO_SET_RELAY commands.[1]
Cockpit does not yet have support for generic MAVLink commands, but it is planned. As far as I’m aware QGroundControl doesn’t support that kind of vehicle control, but from the ArduRover docs it seems that MissionPlanner does.
ArduSub will likely end up moving in a similar direction (because in principle an autopilot shouldn’t need to know about or store the specifics of a given input method/device), but for now things are the way they are. ↩︎