The rust spots, if you observe them carefully, it’s located symmetrically at specific spots only. The culprit is the metal based glue that was used to 'stick' the metal piece to the chassis of the roof. Apparently, Proton is using the 'rejected' glue form Japan. Japan car manufacturers (typically Mitsubishi) found out about this back in year 1996 and have come out with replacement for it. What happen to the left over inventories of the problematic old stocks? Proton bought over and use la. Japanese imported cars < years 1996 and protons < year 2000 have high risks for such rusting problem.
U will have to get a good painter, drill + korek off the glues, sealed them back and repaint. Big headache :)