You start off saying that it’s all the same, even if our perception is altered. By that line of reasoning, yes, matter WAS always composed of atoms, whether we realized it or not. Yes, to God it doesn’t matter, but as previously asserted, OUR perception doesn’t get to define that.
Anyway, the argument is recursive. God constructed the mainframe of “nature,” so however He alters it must also define it. How we see it IS really irrelevant. We don’t really have any say in the matter.