Worked a bit on the enclosure using py2scad (https://github.com/acrobotic/py2scad). This neat module auto-generates the OpenSCAD files allowing for easy programmatic design of a few things. It's particularly useful for box-type enclosures.
The auto-generated files can then be opened using OpenSCAD:
The holes size and position are temporary for now, the next step will be to do some careful measurements of the Raspberry Pi and the USB Hub PCBs in order to adjust these parameters to fit all the connectors more precisely.