A possible origin of the OT/FST split JUST occured to me. In LA X, we saw that the statue was intact (although underwater), and in Ab Aeterno, we learned that the Black Rock destroyed the statue. So maybe in the FST, the Black Rock never arrived, Jacob never took Richard on as advisor, and possibly Jacob and MIB's feud ended decades ago.
The thing is though, I'm not entirely convinced by my own theory. I also think it's possible that the timelines always co-existed, and will condense at some point in the future. The Pauli exclusion principle prohibits two particles from existing in the same quantum state, so the universes can never really "touch," unless there's some perversion of the laws of Quantum Mechanics. They've definitely come close though. The time they've seemed closest was during the 815 flight. Maybe when they get close enough, the occupants of one universe are able to "sense" the other (as with Jack and Desmond on the plane). What I think could happen is that at some point in a future episode, the two universes will again come together.
So the FST in my mind comes down to one of two things:
1: It diverged in the past or will diverge in the future from the OT, and it's being shown as an outcome of some catastrophic event.
2: It always existed and will converge at some point due either to an "alignment" between the universes or to some other catastrophic event.
The first one seems more likely at this point, as it seems to fit the data, but it leaves some things unexplained (like the Jack/Desmond thing). I'm curious to see how this pans out.