So my naturalist view is bottom up rather than top down. It is not that H2O exists and I'm trying to explain if the parts explain the whole. I'm saying the only thing that really exists is the First Cause. Everything else is an artifact (say) originating from different arrangements of this base reality.
I think it misleads us to try start with the concept of H2O and ask, is it made of its parts or is it something more. We should instead start with the base rules and see where they end up. In our universe, we end up with electrons and protons and when they combine in different ways, the behaviors of H and O and H2O emerge. And in general, any universe that starts from the physical laws of our universe but say different initial conditions will likely have H and O and H2O in it (there are caveats but the general idea holds).
