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.
A creative melding of the new multiplexer box with something like this case is exactly what I was thinking. Got a Pi Zero today to test OctoPrint. It's way smaller than a Pi 3, so the new Frankenstein case should be easier to design. Or even attach a minimal Pi Zero case with small M3 screws to the multiplexer box?
Edit: Here is the RPi 2/3 minimal case.