Coming Home - S4-E1
Revealing mistake: This scene of Dawson and Joey in the parking lot of the "Dive-In" was not really filmed in the same location. The show only had the location of the "Dive-In" for a limited time, and had to film all other related scenes in the parking lot of the studio in Wilmington, NC. Any scenes that don't show water in the background; and are just palm trees, lighting etc. were actually shot several weeks later in the parking lot, which was recreated to be part of the beach at the "Dive-In". (00:33:30)
Coming Home - S4-E1
Revealing mistake: In the first scene, Pacey says something like see I think we should probably drop anchor here, have a bite to eat (and other things)... As he's walking around the boat, the camera shifts over and you can see two ropes that indicate the boat is already anchored or docked to something.
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.