The process seems to depend on the assembly plant and year. From my experiences.
For others looking at San Jose cars
I've found them both ways on San Jose cars (cars with exterior color over sound deadener and those with some black spray or body color - over the sound deadener).
It is my belief that some workers stationed at the pinch weld blackout station would black out the rear wheel wells as the cars passed by. In a non scientific study
it looks to be 50/50 with no connection to the exterior car color.
Bottom line for me is that a restored rear wheelwells we don't want to see sound deadener over body color or black with out body color under it. Its all about reproducing the original steps and processes. We've come along way in or understanding of how the unibodies were processed and prepared.