Not sure how it works on other devices, but with the vivoactive, if you have the "default watchface" set, under settings>system>clock, you are given options such as setting colors for that watchface (you can configure it).
I know that there is a plan to allow customization of connect IQ stuff with GCM or GE, but I expect that to be a "longer term" thing. What if the SDK was expanded to allow a CIQ watchface to add a menu to settings>clock, where users could do things like select a color scheme? It would make it simpler than trying to do this with GCM/GE, and it possibly could be implemented sooner. And elimiate the need for multiple versions of the same watchface, with different colors.
Seems the FW already has a logical place for settings used by a watchface, so it would fit in the general scheme.
