I don't believe so. For starters, there is not enough space between the tunnel roof and the surface to support basements and sub-basements of any appreciable depth. Second, the tunnel was not designed with weight-bearing walls and pillars sufficient to support a large building. I believe the only part of the Big Dig designed to support a tall building was the vent structure that was morphed into the Intercontinental hotel, and the cement and steel that went into building that was formidable.
^^ The building wrap looks more interesting than the proposed finishes on the mock-up.