As I understood/interpreted it, the whole of the "alternate timeline in Season 6 was a kind of afterlife where people go after they have died until they are ready to move on. As such, the only people that were definitely "real" were those we had already seen on the Island. (Possibly the whole construct only existed for those that had spent time there?)
I think Jack's "son" was something he needed to work through until he was ready to move on and so wasn't "real".