I once had the opposite problem. It turns out that they use the same policy in that situation:
It was 2004 and I was in Altoona. It was about 1:15 in the afternoon and I was waiting for my westbound Pennsylvanian for Pittsburgh. So a train comes in and without really paying a lot of attention (it was my first Amtrak trip so I was pretty fired up), I climb on board.
Except it turns out that the eastbound Three Rivers was running about 45 minutes late and arrived at the same time the Pennsylvanian was scheduled to arrive. Looking back, I'm surprised I was the only person that did this. I discovered this in under two minutes and immediately found the conductor. I asked if I could just get off at the next stop, because I could easily get a friend to drive down to Huntingdon from State College. She said to hang on and disappeared.
Minutes later, a different person shows up and says "come with me." Seconds later, I was practically hanging out the door of the car while this guy yelled (the wind was screaming through that open door) that they'd held the eastbound Pennsylvanian at Tyrone. He also said this actually happened a lot, because of how close the two trains were. I think there was only about 40 minutes between them on the timetable.
So, and looking at the time table, less than eight minutes after accidentally boarding the Three Rivers, it makes an unscheduled stop at Tyrone, where the Pennsylvanian has been held and I get to change trains by walking a few car lengths on what I can only describe as boulder sized ballast on the NS Pittsburgh Line. I, of course, count the Three Rivers and Tyrone in my travel list.