One of the advantages of a dual-manual organ with pedals is that you can have at least five voices available at all times. The registration buttons are immediately above the keybed and easy-to-reach. There may also be toe and heel switches on the swell (expression) pedal that can be operated subtly, you wouldn't see it unless you're really looking.

He might well be using some MIDI but it's amazing what a skilled organist can accomplish live!