If not properly gotten rid of, rust will come back(under your nice new paint). It may take awhile but will show as bubbles in your paint only it's not your paint(METAL ZITS). God forbid you have any Bondo on top of such areas because it will pop the entire piece of bondo off car.
Primer is not a sealer either. At least as far a H2o is concerned. It is right before painting, but in my case, I have primed parts (on my car) in September and use car every day(rain or shine). I will have to re-work those parts before I get the 'killer' paint.