Unlike some studios, Bones never really tightly defined the pseudo-science behind the Gates, the Contractors, or their powers.
I mean, who ever would have predicted a Contractor who could
recreate the whole world, and populate it with people, just using the info from the first season?
As for Yin, do take note that the Izanagi/Izanami myth
does not end well, with the death of Izanami and the literal introduction of Death into the world at Kagutsuchi's birth. But fret not, as it's likely the myth is simply a template used by Bones in the plot, so it's possible that Hei chose the Third Option again like in Season 1.
Or he could have fried her and ended her misery. In either case, an announcement for another iteration will probably come up next year...