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I've seen this kind of blistering happen before but not had to deal with prepping it. Sometimes there's a lot of resin in the wood that comes to the surface, the best way to get rid of resin is an IR stripper. It might not be the problem but if it is it might be possible to seal it with 'knotting', basically shellac.
I'm not sure Zinsser do but I usually use cover stain. It's not penetrating though. I'm not sure what's causing the problem with your windows though. At least cover stain is useful in lots of applications, its not moisture vapour permeable though.
All coat is the Zinsser all in one exterior paint. I use a lot of it. Its supposed to be self priming but you might have something else going on with that patch on the window so I was reluctant to recommend it.