Here is a crazy idea. have sunroof glass made that will replicate the roof shape in the location the sunroof is going to be placed. Since the sunroof will probably be a popup, slide up style, it seems possible that the strange shape of this glass wouldn't pose a mechanical issue because it isn't having to be stored between the roof and the headliner.

That way, when the sunroof is closed the shape of the roof is restored. I can see this as a legitmate port option or aftermarket item if placement of the sunroof is solidified and made somewhat standard.

It has been said:
Hybrid drivers come in 3 flavors, greenie, techie and cheapie. Pick any 2.
2005 Prius, Melinium Silver over gray, package 5 (AI)