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.
Yeah, you're right. My assumption is that people will do a little cleanup with a hobby knife and ream out the filament path to size. That gives the tightest possible fit around the filament to avoid buckling with more flexible materials. If you print with 0.1mm layers, the mess there is minimal.
I personally prefer to print it upright so the bowden fitting threads come out as clean as possible, and was surprised to see how many people choose to print horizontal instead. I might have added some bespoke support to the bearing pocket if I had known people would prefer that.