Triggering passive Companion Computer

It is fairly trivial to create a mapping mission that triggers a camera at every waypoint, right?

OK, so how would one go about about triggering an onboard computer instead? I could just connect my Odroid to the Pixhawk’s PWM or servo output, as a pseudo-camera – but that seems to be a waste of a nice and comfortable serial connection, and besides, as described in this question I want to signal when the Odroid’s “camera” work is done and we can go on to the next waypoint…

Any ideas?

(And no, I don’t want to set up a fully-fledged mission-control GCS on the Odroid if I can avoid it; I’d rather create the entire mission on the ground and let the Pixhawk control the flight than have the Odroid dole out waypoints one by one. Can I avoid that?)