Quote from the Mass Effect Wiki inbound:Neocavo said:For starters.. in mass effect 2, it was clearly stated that SR2 model of the Normandy was not rated for atmospheric flight due to hull pressurizing and weight distribution. but it was shown in the trailer doing a bombing run? (2:37)
In Mass Effect 3 the Normandy SR-2 has been claimed by the Systems Alliance. Feeling that the ship, being based on the Systems Alliance-designed SSV Normandy, is their property, they have taken it apart, studied it and rebuilt it, adding new parts and opening new areas.
(the details are take from a gameinformer interview with a ME3 designer)
So in short, the alliance took the ship and added new stuff to it!