From the numerous comments here, it's not matching the boarding pass to the flight or gate. Is it just boarding group? Is it that "yes, this is a valid ticket" or something else entirely?
Seems like an easy way to "disappear" - basically book a fight going somewhere, look around until you find a flight with open seats (Southwest would be best as no assigned seating), and then... poof?
That's the question that's been nagging me since the day I read about this particular mistake. I wonder if there are any active public subreddits of airline workers; somewhere where I could hear a first-hand account of what those scanners are checking.