The original material was probably lead, but it might be best to clean/sand and rust coat/treat the area as good as possible, even from the interior of the roof. Then use a quality filler to smooth everything out.
3M used to make a product "AlumaLead" for rust repair of GM lower back glass, in the corners where water would accumulate and they did not paint that well on a vinyl roof car. Something like that, designed for a smaller area spot repair, might work well for the roof/quarter panel seams? You might check the 3M online catalog for more information.
Just some thoughts,
CBODY67