If I try to imagine a god who created the universe the only way I can conceive of it* wanting to do things is by the (mostly) naturalistic process it seems to have used.
If it guided every step and poofed things into place it would be totally uninteresting to it. This way there is a fascinating unfolding of things running on the initial conditions set up.
The choice the creator has is more boredom or an interlude of entertainment.
The universe then becomes analogous to a game of Conway's life automaton game just on a grander scale.
Any other way of doing it would be, in my opinion, much much less fun to watch.