This does look like the only solution for now. As far as I can see this is a design limitation on the current Fritzing version (which I will keep in mind for development). On this version you can’t have separate copper0 and copper1 layers which is mostly sensible but it does break this one use case and I think there needs to be a way to do this. I did find a part in core (the ATmega644) and I can mangle the fzp file to work on 9.3b but so far any change I make to the pcb svg with Inkscape breaks Fritzing (the connections no longer work for some reason). It did however turn up a couple of bugs in my parts checking script that I need to fix so the effort wasn’t wasted. The headers as output in breadboard is probably the best anyway. Any part with overlapping connectors (like right angle headers) is hard to represent accurately in breadboard and the current headers probably do as well as anything.