I use Pepakura for 1mm, 2mm, 3mm and 6mm EVA foam, so I see no reason why you could not use it for sintra. Like you said, you would have to mod the pepakura to deal with the attributes of sintra.
I do not think you could get away with gluing sintra edges together like you can with foam, so depending on what you are building, in some cases it may be simpler to draw templates for the sintra instead of using a pep file for large, continuous pieces. The other thing you could probably do(I do not have a lot of experience working with plastic, so this is just me imagining working with it) is connect two parts together with a backing strip of sintra and then filling any gaps during your finish/paint process. I am assuming sintra is glued with plastic cement.