I think its better if we keep color variables in single group instead of spanning them into components grouping, also I would like to see these color variables being converted to sections like

Primary Colors (the colors which will affect the main look and feel of the site)
Link, Body Background, Navbars etc etc the most prominent components of the site

Secondary Colors (the colors which you can change if you like if not they won't harm you much)
alerts, popups, btns (like warning, success etc), progressbars etc.

Constant or Permanent Colors (the colors which will be okay if you don't change them, I suggest don't change these)
colors applied as an aiding colors, like transparent (applied to some elements so the main parent component's background becomes visible), normalize, prints etc etc.