One option is to apply your color mapping to the surfaces at the end of the model tree after all geometry has been regenerated. Make a feature that is a copy of the solid surfaces. You can then use seed and bound selection to quickly color code the interior and exterior surfaces as needed. You can make it more robust by using datum intent references for the colored quilts but that is not needed unless you are modifying the models often in a way that will alter the color maps.
Using this technique should minimize rework if you wait until the design is ready for promotion to a release level. Here is an example of this technique used to document texture and polish applied to a molded part.
