Kevin, I wish I had taken the time to really document the condition of my rear body section when it went in for surgery the first time. There were a number of very fine cracks in the Gelcoat on the uphill side of the screw holes for each body-side snap because of temperature variances overnight as my car sat outdoors. The material grew and shrank by as much as a quarter-inch each night, seemingly regardless of season. The fix for those involved die-grinding out the screw holes themselves and then filling them individually and sanding the whole works.
If your car was painted, you might want to go back to the shop that did it, or maybe a reliable one nearby, and find out what they would get you to touch up just that section.
If my red car can be used as any kind of a viable comparison, the body's color under the tonneau/top was much brighter than the rest of the car. The red hadn't faded at all, even though the fiberglass had been more abused than the longer, smoother sections.
I guess my answer would be to use the existing tonneau, mark the body for placement of new holes, drill out and fill/sand the old ones and then reset the snaps with the screws in new locations which correspond with the tonneau.
It's easier, and probably more cost-effective, to leave the top alone -- and just have the paint equivalent of a fender painted -- than to have upholstry fixed or its material wrecked.
Key in all of that would be if you have a top; do the snaps on it line up with the car, or the tonneau?