MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
allows you to interact with all your printers via the Cloud, and many other exciting new features.
That is a good idea. I may not get time to do it soon. But that is a good idea. I'll definitely add that feature as soon as I get a chance.
In the meantime, something you can do, is create two models with differently configured holes, and the pin disabled on both models. Then print out the male and female leaves of each model individually. Then you can use a nail or a long machine screw as an external pin, to assemble the two leaves with their differently configured holes. Using an external metal pin would also give you a stronger assembly.