Fwiw I use 3m panel bond adhesive as a first step before filler on rust patches. I apply it with a putty spreader just like you would a coat of filler. My rationale on this is: it has excellent direct to metal adhesion, is waterproof (in case a pinhole exists, it keeps moisture from getting through the repair) and it sands way better than any of the fiberglass/kitty hair type fillers. I believe it would be perfect to seal and dress up those repairs after final grinding/before primer. It uses the same gun as the seam sealer. Regarding the surface rust, I'd imagine a red scuff pad would do the trick, then wipe down with wax and grease remover, or lacquer thinner
Amazon product ASIN B000PEW4MI
Amazon product ASIN B000PEW4MI