I cannot argue that filler to bare metal will stick the best. But, in the end, it boils down to convenience for me. Generally, all metal parts are stripped, media blasted, etc. at one time. Now, if you don't get a protective covering on all that bare metal, you are in for some trouble. So, it gets a coat of epoxy primer. Now, many weeks/months later you are ready to apply the filler. What are you going to do, sand off all that epoxy or just scuff it up and apply the filler directly to the epoxy. A no brainer for me and I have never had a bond failure of filler over epoxy. Granted, I am not whacking my truck on the corner of a desk and if I crash it, who cares if the filler comes off...just makes it easier to repair in the long run.
Just my humble opinion. Everyone should do what makes them sleep well at night.
