This sounds like a variation on the routine I remember boarding the Cascades in Seattle a few years ago: There wasn't an actual boarding pass, but we did have to get in line to get seats assigned and then wait for our section to be called to board.

I have no idea what problem Amtrak is trying to solve here. The NEC runs fine with general boarding and onboard ticket collection; why would you need to mess with boarding passes in stations that aren't as busy?