I like it. Although it seems to be the science fiction version of, “A wizard did it.”
I could go for that. Except one minor change. Since they time travel a lot, and they have their powers wherever they go, then it means that the whole world is in the Matrix.
Actually, that would also explain why there aren’t more paradoxes each time the Fringe timeline is changed. Whenever someone time travels and changes something, the Matrix doesn’t always make all the necessary changes to the timeline, leaving some things intact.