Everyone who goes to the island is dead. That is why women cannot conceive on the island, because they are dead. The island is indeed a place of purgatory.
Think about it. Jacob and MIB's real mom actually died in a shipwreck but is drawn to the island by that crazy lady. She is happy because she needed someone pure but not of the island to replace her.
The ALT timeline is an extension of that purgatory where people can work out their issues before moving on. Looks like Jack had three chances or was in three different ALT timelines because he got that cut on his neck three times this season but he was cut there only once on the island when he was fighting Flocke on the cliff.
The "god figure" of Jacob is always replaceable. The island is indeed a place where science and faith both exist. That's how stuff like the lighthouse and smoke monster can happen. Also, the rules change with each new "god figure."
In conclusion, all of the show has been purgatory (except for the flashbacks). I think the writers realized near the beginning that the purgatory story wouldn't be as popular as they had first envisioned so they spun it in the end with the AST timeline, which in my opinion was awesome. It's like the characters' souls are stuck on the island and some are working their issues out in the real world (ALT timeline)and have a chance to move on.
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