Hello Mike,
When my car was restored in 1999-2001, I wanted to take the "high road" and avoid all manner of bondo or plastic body filler. I told that to my restorer who was skilled with lead and plastic.
What he told me of course, was that he'd do anything I wanted--it was my car and money. Then came the caveat, which is exactly what you discovered. The fluxes are acidic as is the metal prep prior to fluxing. Unless you are ***perfect*** and few people, even the best are, you might likely get the tiny blistering you describe. This is EXACTLY how he described it to me--what you saw. When you use lead or body solder cleanliness is of the utmost importantance.
Now, where there is a lot of sheet metal replaced there is always some filler--not to fill in dents (that's the bondo we are all afraid of) but to fill seams and other minor imperfections. Modern plastic fillers in the hands of a master are great. Lead is great too, but you run that risk you so painfully discovered.
With all the time and money in a good paint job, and all the post-paint work as well, lead was not chosen. I have no blistering. Won't likely get it either. While the concept of lead sounded good, I'm glad it was not used on my car. And yes, I believe it is the fluxing causing your issue. There are also certain places where lead is preferred--there's a ton written about it, do your homework.
The problem with bondo is it is so easy to use, it has been used a substitute for replacing sheet metal. That's where it gets a bad rap. But it isn't the plastic that's the problem--it's the cheap owner or the unscrupulous body man trying to cut a corner or fool someone.
Michael Salemi
1969 280SL
Signal Red w/Black Leather
Restored