Looking at the inside of the shell won't help explain the color change. The inside received a gray wash coat before the exterior was printed. Print coverage on the inside of cars produced at this time frame would have been the result of a misprint.
Lionel printed shells in one print run, cupolas in another, roofs in another, etc. That being the case, the cupola and shell were printed at different times or on different printing presses, perhaps with the same batch of "ink" or perhaps with ones containing essentially the same ingredients.
I suspect that there were more than a few cars that have exhibited this color change and would not be surprised that some non standard ingredient in the "ink" formulation for the print runs at the time the car was manufactured was responsible for the color change over time.