It took 45 minutes to notice him? I am assuming then he wasn’t in a jump seat in the cockpit.
Invisible Boy can become invisible, but only when no one (including himself) is looking.
“It took 45 minutes to notice him?”
This “jumpseater’s” credentials should have been presented to the Captain well before departure. The Captain may or may not permit any given “jumpseater” a ride; but, if permitted a ride, the Captain may or may not allow the rider to take an empty seat in back. This appears to have been a breach of flight security.