"The Buddhist position presupposes that we can know that there are atoms, but claims that the composites we take to be made up of atoms are unreal.
"If they are unreal, then of course we cannot be said to know of them through perception. But the atoms are not perceptible either. So how could the Buddhist know of them any more than he knows the purportedly unreal composites? In fact it is only through the composites that we can know the atoms that make them up. Hence the composites must be real."
The Buddhist argument doesn't say that the composite isn't perceivable or doesn't exist, just that it only exists conditionally. Nobody denies you can't see the composite.
It's important in these conversations that the Buddhist position is always one of soteriological convenience. The point of conceptually separating conventional and ultimate existence is to point out that your mind and identity exist only conditionally. The suffering you experience is part of this conditionally existing group of mental processes. So therefore the causes for your suffering can be removed and that will remove the suffering which is conditioned on those causes.