Yes, atoms are made of smaller parts; electron orbitals change chemistry based on their distance from the nucleus, nucleons change the chances of emitting radiation based on their distance from each other, and quarks greating increase their mutual attraction based on distance.

The relative distance between fundamental particles is governed primarily by forces which don't seem to have changed much since nucleosynthesis. If expansion doesn't affect any of this, then saying things governed by forces are expanding is nonsensical.

I can see a perspective where time is slowing down, reducing the effective range of the forces and letting all matter shrink to fit the changing effective distance, and leaving unbound matter to appear to expand. However, I can't see how this would be meaningfully different from an expansion of all space, not how such a difference might be detected.

Regardless, the distances within atoms continue to behave consistently, while the distances within galactic superclusters do not.