Three things.
1. Most bondo doesn't stick to paint very well, and is designed to be applied UNDER the paint. There are a few thin catalyzable skim coat compounds that can go over the primer that are bondo-like but are for minor fubars in the primer.
2. Buy the non-porous kind. I can't tell you how much rust I'v found under the porous bondo. Read the can to see if it is porous. I like the Evercoat products.
Here is one that is non-porous.
Evercoat Metal to Metal. They seem to have dsicontinued the other non porous one. It contained styrene.
3. Most primers are porous. After spending all that money and time on attaching metal flares, you need some decent non-porous primer like Dupont Variprime. It's a 2 component self etching primer that sets up like a rock and laughs at rain. You have to spray it and it is baby poop brown. The grey and red crap can allow rust to form remarkably fast- particularly if it comes out of a spraycan where the paint dries as little balls in the air and kinda sticks together on the metal as a stack of porous paint balls.
Ken