Consider the following:
Short of a nuke, both Grand Central and NY Penn Station are far away from Wall Street (a high value target). Washington DC is fairly short to the White House, Congress, and the Supreme Court (all high value targets). Yet Amtrak has a unified-for-uber-traffic-stations policy to force you to line up. Washington Union Station has it, Philadelphia 30th Street has it, New York Penn has it. I bet Boston South Station has it too.
So it's not security. What could it be?
The only time it makes sense is when an equipment change or restock occurs. I can see a restock at WAS and NYP. I've seen the engine change at 30th Street PHL for the Pennsylvanian, and I think they do a crew change and restock as well. You got carts going left right and center, and having people in the way slows things down because safety first and running over people delays trains and costs more money. Besides, on certain tracks in WAS, the platform is never wide nor high enough. Thus, it's a safety issue... and I think MARC presented it as that when the change was announced years back.
Grand Central can get away with it because it's trains are just hauling humans. Nothing that needs refreshing -- that was removed decades ago. The only carts needed are for helping elders and emergency crew, which flashing lights and sirens. People know about those. Amtrak is doing a lot more at those stations, and thus it can't.
The other way of arguing it is "Why doesn't BWI, Baltimore, New Carrolton, Wilmington, or Newark Airport do this?" Simple: The trains aren't getting refreshed/reloaded/reconfigured. They're just passing through. Stop, unload humans, load humans, go. That's it.