Howdy Phoneman and welcome to the family of 'Bolts'. I wish I could answer your question about the rust coming back, but I can't. Currently, the cab is only primed with Rust-o-leum Wet Sandable Primer for now, no paint yet. I wire wheeled everything, even the areas that I knew were gonna be removed due to rust. I did come across some areas of pitted rusty metal and the wire wheel worked very well. Most of the pitted areas on my truck that I felt were still considered reusable metal are inside on the floor under the seat. I was planning on coating that with POR-15 or Zero-Rust. That'll put the brakes to rust coming back. The exterior pits on the cab, mainly on the roof, will be skin covered with filler, primed and painted. What I did on the roof was use the wire wheel, then used a DA sander with 40 grit to smooth out the pits the best I could. I'm sure as long as the pitted areas aren't too thin and primed properly, there shouldn't be a problem. If the pitted areas are too thin, you may want to consider replacing the metal. There are alot a guys in here that can help more on this topic then what I can offer.
Hoped this helped ya.
Take care
~Ron