it might very well be that all Oxygen atoms in existence are physically the same in some ways, but we have no way of actually knowing. this doesn't mean that there are 'individual atoms', but it doesn't negate it either.

True (only) in the sense that our numbers are part of our map and not the territory. In the same sense we have no way of actually knowing there are patterns in the universe appropriately named Oxygen. Or Frog.