I agree definitely that Aerobody cars look good regardless of what color the rub strip is....
I too have an Aerobody installation manual. There is no mention of painting instructions. However take a look at the pictures shown throughout the manual (like pg 23). It shows the rub rail in black.
My cars Aerobody seems to have been dealer installed since it is not specified on the Callaway Window Sticker and hence not a valid example of what Callaway specified. However, 91Callaway recently posted his window sticker which shows that the Aerobody was a Callaway option for his car. His car's rub rail is black. Speedsters were definitely Callaway installed Aerobody cars, the rub rails are all black except one (see bottom pic).
Keep in mind that the point of the rub strip, as on a boat, is to protect the body paint from scratching by things that might rub up to the car like a shopping cart. If the rub strip is painted the body color then it would be easily scratched and thus have no purpose on the car.
Looking closely through the Speedsters, the only exception that I have seen is the Red SuperSpeedster. Was it a personal decision by the owner? Was it a repaint? who knows..... I certainly would not care if I owned it.
-Luigi
:cool