OK, so I may be nitpicking a bit here. However, there is a subtle but important issue here.
If you take a carbon atom and arrange it into a diamond structure, you get a material with a particular index of refraction. Now, take the same carbon atom, and arrange it into a graphite structure, you get a DIFFERENT index of refraction. One can do this with silicon too. What this means is that for the same, identical atom, different arrangements can produce different degree of transparencies. The point here is that optical conductivity in solids isn't usually due to absorption by the "atom" in the material. If it does, then both diamond and graphite would have the same index of refraction.
What is relevant here is the crystal structure and thus, the phonon modes available in that particular configuration. The optical phonon modes (as opposed to the acoustic mode) greatly influence the optical properties of a material. These lattice vibrations (phonons) are external to the atom, meaning it doesn't involve atomic transitions. In an opaque material, light that impinges on the material are absorbed by the lattice in these vibrations and converted to heat. In a "transparent" material, these phonon modes are available for excitation and retransmission.
Now this mechanism isn't similar in atomic gas where light has been "slowed down" to 0 m/s. Here, the mechanism is more exotic (if that is possible) than what I've described for solids.
Zz.