xdv8

The two sides of the coin I see from here are that you want to stop the rust before it goes too far but if you knew that you would be putting a vinyl roof on it would you paint the roof to the same standard as the rest of the car? You could try and remove the parts of the vinyl and repair then cover back up or take a gamble and remove and hope that it's painted but then you will have to match the paint once the repair is done. If it were me I would try the repair then recover would be neater in the long run.

Sorry double post

Last vinyl roof I removed was on my old gxl and it wasn't painted to the same quality as the rest of the car which was resprayed about 4 years earlier. The paint stayed stuck to the metal but the glue took forever to get of without damaging the paint any further. If I was to so it again then I would leave it till I was ready to fix the rust and paint the car.