To me it seems that it was definitely supposed to be the same place. The hallway, the same desk at the gate with an orderly, and the fact that Smith is saying 47 was there before.
Why 47 doesn’t remember initially? Either his memories are blocked out because of traumatic experience – after all, he doesn’t immediately recognize Covacs, and the fleur-de-lys at the gates seems to hint at a certain connection to this place that 47 doesn’t realise yet. Or devs just didn’t think too hard on that…