Going
way back into the past (or one day, depending on your perspective), the physics model we're using is based on
Schild's Ladder. The plot of Schild's Ladder is about an expanding patch of new laws of physics accidentally being created inside our universe, called the Novo-Vacuum. Eventually, some people on the research station floating just outside the Novo-Vacuum figure out how to translate themselves into the new cosmology. The research station is called
Rindler. Combined with this bit:
which confirms that where we are now has had causal contact with the physics Kagutsuchi merely emulates, I think we are currently inside the Novo-Vacuum, or something similar, that was created (but presumably not controlled) by the people on board
Rindler. This would explain the frequency of both humans, and normal-physics emulations.