Why John, Sun, Frank and Ben are seperate from the rest and why John is different now
John’s suicide note said ‘I wish you had believed me’ so when Jack read this he then knew John had made that wish (and maybe even started to want that himself).
Ben said in season 3 that there was a metaphorical ‘magic box’ that could provide you with whatever you want – I think that magic box is the island and that people who are special however John and Ben are (possibly Jack too) can manifest what they really want and that either Ben or Jack’s wish for Jack to have believed John has come true and they are in some sort of tangent reality where they are the only ones who survived.
It’s also possible that this is why John is so different because he would have become leader and gained a much greater understanding of the island. Another thought which followed this but has no evidence is that the island itself may be a manafestation