Sorry to say, but I think that Amtrak's rationale for boarding, as in the blog mentioned in Slate, is total bunk.
Amtrak has the "line up and wait" boarding process even in Charlotte when boarding the Piedmont, which is a 3- to 5-car train. There is plenty of room on the platforms. I think that it's just for the convenience of Amtrak's personnel--not the passenger.