The problem you have using a material in one section would be where to finish the material off to, the Challenger has a distinct body line running over the roof and any padding would hide this line, the alfoil tape is their to stop the savere sink back of the vinyl over the holes but you still can see where the recesses are on a original car, i know guys who have filled in the area around the rear plug with different products to hide the factory faults, but they are what they are.
Some more SE owners with close up pictures would be great, i still to this day have not seen a puffy vinyl roof on a Challenger or the rear section.
When you guys are at Carlisle next, can you make a point of going up to each SE you see and feeling for a padded roof and then ask the owner if they are near by if the roof has been reskinned or not and if it is in fact padded underneath. This would help in the conclusion with restorations.