The only way moisture can get behind the filler is if the filler is exposed from behind the panel like if moulding holes are filled in or through any holes that aren't welded up, which is going to cause problems regardless of prep to the finished side of the panel. I like to prime before filling because most of the stuff that I work on comes from the rustbelt and has surface rust, pits, etc... so after I kill the rust with ospho I etchprime then fill. If the panel is rust free then priming before filler is a waste of time and materials.
