You're right, Instant Terra doesn't support color maps for the moment.
But it's in our short term roadmap (i.e. the development has already been started): you'll have the possibility to import a color ramp, or create one from a color ramp or from a mask. Then you apply this color map to a terrain and the color map will follow the transformation applied to the terrain (translation, rotation, scale, blend with another terrain, etc.).
Edit 2019: Color maps and blend of color maps are now supported.