I'm not really concerned with judging for the 307 Coupe, but rather with preserving the historical integrity of a car that has not been messed with (the SS above was ridden hard and put away wet so I didn't mind adding a few items here and there) and has low mileage. I know that if I keep the dealer installed vinyl roof then every time the car shows up somewhere somebody will feel obliged to point out that it is not a correct roof...so to me the question sort of boils down to whether or not I want to listen to it....but it also had relevance to our discussion.
Regarding people pointing out the vinyl roof; just document the cars history with a story board explaining the cars unique and interesting history. This way you don't need to repeat and explain this issue over and over.