I've always wondered why when passengers are boarding the aircraft, the doors to the cockpit are wide open and everyone really has access to the pilots, cockpit, controls, etc. It is only when the plane is ready to move that the doors are closed. If it were up to me, I would have the pilots locked in the cockpit before any passengers were allowed to board
I guess if the people planning to take the plane can somehow get rid of the pilots in the few minutes they have and then taxi a plane to the runway, you might have a problem.
If the plane is on the ground and the cockpit door is open, I see no problem at all. Like you said, the door is closed in flight and I think the purpose here is to make sure the thing isn't used as a human controlled flying missile.