Given the history of this specific project, and the fact that one or more of the changes may affect the building's height, I can understand Landmarks' and UDC's feeling the need to take a look at it.
I remember the Union Transfer fiasco too. My recollection is that the developer got off with a slap on the wrist, and got to keep what amounted to an extra story in the height of the building.
I think he even got severely scolded by some city officials, by golly! Bet that taught him.