Wood does rot when wet (and enclosed and light tight). What happens to RV's they rot. The reason why your aluminum roof perforated in the first place was water under it and the water coupled with the mold, attacked the aluminum from the underside causing corrosion and your hole issues. It corroded from underneath not from the outside.
After you mitigate the intrusion issue and only after, I'd repair the perforations with sheet aluminum sealed to the original roof with either Dicor or Sikaflex. Don't think Bondo is the correct solution to the repair.