Body fillers stick to the metal through mechanical means. The smoother the metal, the less perfect the adhesion will be, which is why the instructions always tell you to rough-sand the metal surface. Those scratches allow the body filler to stick very well and for a very long time, assuming there's no rust layer.

Since we know that fillers stick best to metal, it stands to reason that spreading them over primed metal surfaces can lead to separation later. That's true, but if the surface is still scratched and rough the filler will tend to stick extremely well. If you use an etching primer you must make sure it is properly cured before using filler. Otherwise, the phosphoric acid vapors left over can slow down the cure of the filler resin.