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.
I am currently not planning to modify it in that direction. I am busy stm and it will end up being to many derivaties that way.
But please feel to modify and publish it yourself. Thats the reason why all the source files are published as well.
But another approach: Would it work out if you put the casing upside down? I think it might be flush with the extrusion then?
But i could be wrong with that.