Well - think about it this way. You know how we had that mission to travel several hundred million solar sweeps in the past? Let's say that, in linear terms, that is the earliest point that the timeline experienced external meddling. Any timeline that experienced no meddling would have to branch off at that instant, and have no other time travel events for the rest of its cosmic lifespan.

So it's entirely possible that such a timeline exists, but given the Initiative's total irresponsibility with the timestream, they probably either don't exist or never developed a time machine. Or that timeline could have been terminated a million sweeps before it ever got to that point. But at any rate, it's impossible for a timeline like that to intersect with ours in any meaningful way, since the key variable is time travel itself.

My point is that, for all intents and purposes, any timeline not affected by the Initiative's time travel may as well be an alternate universe.