I really liked the roommates and their interaction with the Scoobies. As I said I hope it was just something that was bothering Xander that he wanted to get off his chest and nothing else. If it is what I think it is then it would completely undermine the heart to heart that he and Buffy had last season and I don't think Joss would do it. It's possible that I just overreacted to a scene that will pay off later on.
I can't see it as anything but a mislead.
BTW I asked Scott Allie how much time passed between #40 and Freefall. His answer was "More than a month, less than a few months". You can see the rest of his Q&A on the Slayalive forum.