I just re-watched the episode and I was looking closely at the alt timeline. I noticed how jack lost his fathers coffin. And the island is underwater. But could this be the world trying to course correct itself. Locke lost his knives which would give him a reason to go back to australia. Same with jack. How the charlie knew he was supposed to die. As if he is the old charlie. And desmond was on the plane then he disappeared.
Could they be the people making sure everything goes as plan. Sorta like Mrs. Hawking made sure desmond did go to the island.