Yup. Everything underneath has to be stock to be purely legal*. The rule has always been applied (I saw this done several times in the 80's to ITA Rabbit GTIs, which were RARE without sunroofs*) that all you can do is peel off the
skin of the roof and replace it with a non-sunroof
skin. - GA
*We're working off the assumption that the vehicle in question - whatever it is - is not available on the same spec line as a non-sunroof car, e.g., ITA CRX Si. The GTIs in question could, legally, replace all sunroof-relevant bracing with non-sunroof bracing, as the GTI was, theoretically anyway, available without a sunroof.
On edit: The requirement for metal of same material was purely intended in regards to parity of the rules and safety. They wanted to remove the sunroof and all mechanism for safety, as you don't want removable/slidable panels loose inside a wrecking car. But, you don't want to give those cars any performance advantage or disadvantage versus non-sunroof cars, so this was the best way to make them easily and cheaply as close to a non-sunroof car as possible.
Shit, I don't think carbon fiber was even INVENTED when these rules were written (

), and certainly not within the mindset of SCCA Club Racing (you know, back when showing up with your car in a trailer was, like, showing off...?)