As for whether or not it all points to God or not. Who can say.
I don't see how the old system suggests their is no god either.
All it would show is that god has a maturity level that is much higher then your average Sim City player.
If anything, to me the old science seemed MORE god friendly as it pointed to everything being exactly "perfect". Miracles can be eaisly proven in such a world, as things that just can't happen do.
You can say the odds are agaisnt humans existing and everything being just right so we can exist... but the problem in a world that's nothing but probabilties is just that... probabilties.
Even the most unlikeliest of circumstances can happen, and will... given enough time.