Nick, the answer to question 1 is to first use an encapsulating sealer like Master Series Silver or Eastwood Sealer. This will stop any remaining rust from getting worse. I wouldn't use the Bondo Brand plastic filler. I would use a better brand. I don't have one to recommend but Eastwood sells it. Once you have used the filler and have it where you want, seal it again to keep moisture away from it.
Question 2 is yes, the 2 different brands have reacted to each other and caused the issue.
