it won't be surface rust though. the pannel will be rotten through. i bet if you wire brush it you will find holes and you can't paint a rusty hole. then when you remove the headlining and sunroof and have a look insude it will be rotten needing a new pannel.

i think with the carbon roof you just cut the roof out leaving a lip all the way round and then bond the carbon roof on, fairly easy. you won;t even have to get it painted straight away being carbon so you could do the "repair" and then get it painted some time in the future if you wish. could always use it as a theme for the car.