You can paint over bondo by the time it's sanded and worked. When you're done working it (assuming you've used 80 grit then maybe 180 then maybe 240 or 320) it should be ready to paint. It does suck up the paint a little bit. I fixed some dents on my roof before starting with the canvas white, and after 4 coats it's still a slightly different surface where the bondo is.

I didn't have much rust so I can't help you there.