I haven't been on an Amtrak in about six months, so it may have changed, but where were you boarding? Was it New York? Boarding in NY is slow and structured, but when I've boarded in Back Bay (Boston), Portland (Maine), and Providence, it's the better way that you've mentioned.

They make everyone rescan tickets for the North East regional in NY also, if you're just passing through. It's a bit annoying, but I wonder if the traffic getting on and off is too great in NY to be able to do that. I have no clue, though.