I used a few different types of spray primers, a couple brands of grey and another brand of black primer. no issues in those areas. primer is a must-use for over bondo, otherwise the bondo will suck in the first few layers of good paint you roll onto that area.

Another idea - rather than using primer, you could use a similar color rustoleum as the paint you are putting on. This might be better because the gloss will be increased and you can see if the bondo is straight or not.

So for me I'd get a can of white rustoleum gloss spray, put a couple coats of that over the bondo.. then smooth it out, feather it in and then roll over everything with the brightside.