I'm beginning to wonder whether the residential addition planned to sit atop the historic headhouse isn't being built to its originally designed height because Riverside (the developer) has decided to save some of the available square footage for use in Phases 2 and 3.
Riverside/Union Station has 3.1 million square feet to play with, short of purchasing more square footage from the city. The apartments being built in Phase 1 will draw many because of its unique location, but its odd configuration probably means some amenities that are now demanded by upscale renters, like a pool, may be difficult to accommodate, thus limiting the pool of potential residents. The fact that the building is essentially hollow means they aren't burning a lot of that 3.1 million square feet. The original headhouse (which does not count against the 3.1) and the planned structure combined is only 1.1 million sq. ft.
Phase 2 (Amtrak parking garage immediately south of the headhouse) is slated for office. Initially proposed as twin towers (at 750,000 sq. ft each) as part of Goettsch Partners' original master plan, now appears to be a single tower at 1.5 million sq. ft., if recent articles about the project are to be believed. The West Loop is booming, both as a residential neighborhood and as a business destination. I could see Riverside gambling that more of the available square footage would be better spent on the office building, instead of rental units across the street. No renderings were released of Phase 2 yet, so nothing etched in stone.
Phase 3 (over the south tracks) might be limited by the engineering challenges that building over tracks might present, but Riverside recently completed 150 N. Riverside in Chicago, which was built over Union Station's north approach tracks. The building is 1.25 million sq. ft., but due to its cantilevered design, its footprint only occupies 25% of the lot on which it's built. Phase 3 is envisioned as residential or residential/hotel. Long-term plans for Union Station include the possibility of a new concourse over the south tracks (300 South Riverside plan). No idea whether they'd reserve square footage for that possibility, or even if they'd have to.
I also don't know whether the agreement between Riverside and Amtrak cements in place the percentages of residential/hotel/office to be developed, but I would hope both parties are savvy enough to keep their options open. Developer 601W is well on its way towards the restoration of the Old Post Office, which will soon dump another 2.8 million sq. ft. of office space onto the market, and is located just cater-corner from Riverside's proposed Phase 2 office development. That might prompt Riverside to go back to the original two tower concept of Phase 2, but one tower office and one tower residential. Who knows?
ETA - There is always the possibility the shorter addition is in answer to engineering problems. Each side of the four-sided office structure that sits on top of the Great Hall is 50 feet deep. At the presentation for the addition, the architect explained that 50 feet isn't deep enough to accommodate a double-loaded corridor of rental units. The solution was to design the addition so that each side would cantilever over the edge of the headhouse by about 10 feet and also intrude into the light well by about ten feet, thus providing floor plates that are 70 feet deep, making a double-loaded corridor possible. That might also explain why the addition's appearance is akin to stuffing 10 pounds of manure into a 5 pound bag, but I digress. Perhaps the cantilevering places stresses on the existing structure that it wasn't designed to take, and the engineers felt going shorter was the safest way to proceed. Just a wild *ss guess on my part.