The hardening part of case hardening and the coloring are two separate steps. The carbon absorption occurs at higher temperature and the metal crystaline structure "set" by rapid cooling to below critical temperature (quenching).
The colors form on the metal surface from a thin, loosely bound layer of various "oxides and stuff." The "stuff" comes from the charcoal, bone, and quench water. Color formation is at lower temperatures and can be done independently of hardening.
Case hardening does not automatically produce a colored surface and a colored surface does not automatically indicate hardening.
The hardening is pretty much science. However, since people don't agree on the aesthetics of colors (brilliance, hues, etc.) and coloration patterns (stripes, pools, etc.), coloring is the domain of the artist.
