I can imagine a world (maybe not ours) where there are no atoms, just ideas, in God's mind, and the ideas are interacting and are formed by something completely different than atoms. Like our dreams. Are there atoms in dreams? What about a dream of a person that turns into a bird and flies through the emptiness of space and disappears into a mist that starts dreaming of a person.......
So the question still remains and it is still open to discussion even if you insist that any universe must follow a rule-based system. Moreover, that would imply the existence of these rules in a kind of platonic sense. How would they give rise to a universe? This is not as simple as you make it to be, at all.
I think you're mistaken about philosophy; maybe early 20th century philosophy. Right now it seems like there's lots of interesting debates going on. But I'm just an observer.