So all of this season's alternate universe was the after world. Some think that means everyone died when the plane crashed, especially since Jack dies in the similar position as the series opens (Jack laying on the beach). On the show after the finale, Jimmy Kimmel said he thought Jack died when the plane was rocky (and then evened out, thus the transition to the other world), and that confused me more. I think everything that happened on the island happened, and Jack died just like we saw.
I guess the mythology of the island doesn't need to be completely explained.