Unless I’m missing something (which as you know is always possible 
), I think the two layer approach is only needed for parts with copper logos on both sides. This is a png from gerbv with the corrected jack part above with only copper1 defined. The one on the left was switched to the bottom of the board in inspector and the one on the right is the default top of the board setting. The pads aren’t duplicated as far as I can see. Am I missing something here? I suspect the addition of the copper0 layer is what causes the pads to be duplicated and may be fixable by removing the unwanted copper layer definition in the fzp file (although you would need to do that by editing the file I expect).
Peter