In that regard, color doesn't exist on its own but is an emergent property of the wavelengths of the electromagnetic spectrum, or at the very least of the way our eyes perceive it.

The carbon case is that light passes by, it's beyond me but that comes down to molecular structure and not individual atoms.

Atoms actually have color, just not one. Atoms have these electron orbits, if an electron gets hit with the right energy (which is actual discreet energy levels) the electrons can jump to a higher orbit. It can then fall back, and emit light of a specific wavelength corresponding to that energy difference. It's how spectroscopy works, by testing all visible colors of light (and probably outside visible spectrum too) you will get dark areas in the color band where said light/energy was absorbed.(because the emitted light of the same type that hit it goes off in random directions)

Each atom will therefore have a unique color strip for identification, so we can say atoms have colors!