Here is what I would do.
Grind all the rust off then shoot the etch primer over the bare metal. When its dry rough it up with some 80 grit and then apply the bondo. After you have the surface shape the way you want spray some high build 2K primer. Wet sand with 400 grit then 600 to get the surface nice and smooth. Now your ready for your base and clear coats.
Many people don't mind putting bondo over bare metal, that's pretty much old school but....... bondo sticks very well to roughed up etch primer and the primer will help seal the metal from any moisture that might get through the bondo before it is painted. Bondo is very porous and wet sanding and even high humidity will allow dampness to get through and begin rusting the bare metal again. Using the etch primer first eliminates that problem.