Ah, a mall. I'd always wondered what the upper levels of the station had been.
The building looked to me like the original was the facade that we see from Columbus Circle. And behind was a 2 level add-on (above ground). And there's those restaurants on the 2nd floor that overlook the original main hall.
The basement had most of the mall, such as the movie theater. The big drug store is still on that level, as are the intriguing old portal gates behind the fast food counters. Apparently there's a service corridor running transverse back there, but the portals once provided access from below to the main level platforms?
The upper level, above the main level, has two basic restaurants, as well as the some of the same semi-high-end retail as the main level, where such retail, with not many customers, blocks the congested queues to the Virginia trains. Those queues go to the annex concourse over the lower level tracks. That concourse has enough space once you get there, but is decidedly not historic, just flat walls and no shops or seating.
The retail shops do not entirely block the Virginia queues, since there is room between them, but there you have to wait politely until the line gets shorter. Amtrak could either take down some shops and use the main hall for queuing, or open up the unknown (to me) floors on the east end of the main hall.
The upper level is spread out around an open atrium, and designed in a sort of gaudy 1980s vibe, but overhead and to the north are beautiful elements of the historic station. You can see close up the backs of the famous guardian statues that look out over the main hall.
I finally read the Washington Post article, and between the lines it's just down to paying the former leaseholder now, between $250m and $750m. Work can proceed, as long as it doesn't cost much. The stakeholders for the station mentioned are Amtrak, MARC, VRE and Union Station Redevelopment. Not mentioned is the Commission of Fine Arts, usually cited as "powerful."