My body guy and the local auto body supply house swear by epoxy on metal, then filler, then high build primer, then epoxy (or sealer) then paint. They tell me you want a sandwich (where epoxy is the bread, and filler the meat) This protects the filler and ensures no moisture ever gets to the bondo, (look at prev bondo jobs where it went on metal- see the rusty areas under the bondo? there is the issue) It will bond pretty good either way, but bondo popping loose seems to be a thickness issue rather than a scratch issue. Ever notice most bondo failure (less than 1/4 in thick) comes in the form of little bubbles? When you dig it out- theres a rusty spot in/around it- this is moisture that was absorbed, and caused the rust, and then we see the end result. Had there been a barrier (epoxy) on the metal, moisture would not have mattered. This is how this was described to me, it makes sense to me and seems to match what I have seen. It might only apply to cars in my area, and maybe not in the NE or Seattle, or even arizona.