While I've seen this sort of theory gain some popularity over at ZU (
see humulation timeline) I've never been a fan myself (nor am I a fan of the GT timeline). To have timelines merge... it just seems so unnecessary.
Anyways, the OoX story wouldn't make much sense if it was 2 stories happening simultaneously and somehow leading to Ganon, as it requires that one story follow the other in order to reach the conclusion (due to references to the past game and appearances of past characters). If it were to merge (with each timeline starting the story with a different oracle game) it would then have to happen at the one point that either playing order leads to, the Ganon fight, which is the same in each order
So rather then this
OoA-------OoS
..........|.........
.......Ganon......
..........|..........
Rest of the Timeline
Which would be impossible
it would have to be
OoA..........OoS
..|..............|..
OoS-------OoA
..........|..........
.......Ganon......
This would then take Farore (who through the password system was able to manipulate time ["Do you know the secret to moving through time?"- Farore]) out of the equation altogether (as she plays no part in the final battle), and there would be nothing forcing a timeline merger.