I think the creators story is done well.
You critique about passangers being gone is a weird one, because they probably arrived to their destinations. If you ever rode a train you'd know, if you taking a train to the end destination, the train might be completely empty by the time you're there.
Also, your 'improved' story has way bigger flaw. If a train security asks for the bag, why would they then thank a passanger for doing what passanger supposed to do? I'd be sussed out.
I genenerally liked the story as it was made originally, but I see your point about making it less obvious, though I wouldn't say it's better. Pretty subjective taste thing.
Don't mean to come off rude to you, just want to add counter-opinion to your opinion. Because I liked the game as well! And good job reporting all these bugs.