I should have been clearer about procedure maybe...
Yes I apply more epoxy over the filler. Anything that might absorb moisture gets epoxy over and under.
As I stated earlier I also use the epoxy for my 'high build'.
3 epoxy = 2 normal build.
As for rust under filler... I believe since filler is an exothermic reaction (gives off heat) the potential for water vapor to form and get trapped is/was the problem.
That and not cleaning the surface with a good wax and grease remover... I read recently a guy doing a new panel and stripped the factory coating (as a precaution) only to find rusty finger prints under it...