You have the mistaken impression that the answer to why "Photons Move Slower in [any] Medium" is primarily the result of "the collective properties of the [medium] as a whole, not the properties of the individual atoms". Quite simply, it is false (not just naive) that "disturbance of the lattice [..] is the origin of the apparent slowdown of the light speed in the material".
Light is slowed even in a dilute gas. Slowing of light requires only one property: that the medium has some small ability to be electrically polarised. All atoms have this property individually (a small perturbation in electric field causes a small perturbation in electron distribution around the nucleus, even without actually "exciting" the electron). [See reference