Hear me out. Could the parallel timeline glimpsed in the flashsideaways be instead a product of the continuing story in 2007? As in, the detonation of the Jughead didn't result in the parallel timeline (suggesting Juliet's "It worked." refers to something else), but something we instead have not seen in the 2007 on-Island time? Some ideas:
1) Jack's red mark on his neck is a result of something done before the parallel timeline came into being.
2) Darlton has pointed to New Otherton on the submerged island as a suggestion that Jughead's detonation in 1977 did not result in the island sinking.
Where could this be leading? Perhaps anyone present on the island when the parallel timeline occured, or anyone who has ever been on the island,(including deceased individuals), slowly comes to remember the previous timeline?
But the ultimate question is, what does result in the parallel timeline coming into being?