Continuity mistake: In "The Te of Pacey", Pacey's birthday takes place in winter - it is snowing and everyone is wearing heavy clothes. The other episode featuring his birthday, season 2's "Crossroads", takes place in summer (everyone is wearing shorts and light shirts).
Factual error: When Joey and Pacey go down to the Basement to talk, they catch Dawson and Gretchen kissing on the basement couch. They are lying on the bottom cushion of a couch raised above the floor. But when Pacey is talking to Gretchen about it in the kitchen during dinner, he says something about "Catching her and Dawson making out on the Basement Floor". He definitely uses the word floor, but Dawson and Gretchen weren't down on the floor - they were up on the couch. (00:23:25 - 00:26:05)
Answer: It's the same apartment Joey had in NYC. Comparing it to the beginning of the Finale; you can tell it's exactly the same location, furnishings, Plasma TV etc. Apparently Chris was only living with her at HER apartment, and now Pacey has taken his place at the end. I guess this implies Pacey successfully started his own restaurant business in NYC as he had dreamed, to be with Joey.