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 sent them feedback, I'd suggest doing the same, maybe someone picks up.
In the meantime, install OpenSCAD, open the *.scad file, press F5/F6/File->Export. Much faster than Customizer anyway.