Hi John,
My experience is small, but I can tell you that my body man, who is a professional restorer, always has the body media blasted as it is, before any repairs. When done, it identifies all the areas that need attention, some that might have been hidden before blasting. After return from blasting he sprays self-etching primer on the entire body, then proceeds to do whatever body work is required, including cutting out bad panels and replacing them. As each area is repaired, he sprays it with self-etching primer to prevent rust and moves to the next area until all have been completed.
There are probably different opinions, but this is the process that I'm familiar with.
Cheers!
Chuck