From, my experience, thus far from drawing acrylic cases, the distance between the top of the mounting plate to the top of the base plate has to be a bare minimum of 9mm, since cherry spec says 8.3mm to the pins (5mm from switch plate top to PCB top and 3.3 from PCB top to pin bottom). Now, on my acrylic cases, the layers are generally about 2.8mm thick, so I use 4 layers besides the base layer. The height of the Teensy is about 6mm minimum (1.6mm PCB, 4mm USB connector, some pins), which is also the height of the TRRS connector. This is one of the problems with the ErgoDox, the Teensy mounted ontop, means you get wasted space, both above and below and the mounting plate.
So taking the switch mounting plate as base, I think 2mm above up-till the bottom of the top plate should suffice (Flush mounted Teeensy), and 10mm below up to the top the base plate.
Upto 6mm for TRRS, 4mm for USB above top of PCB level is required to be cutout in the layer for access to connector, and 1mm below top of PCB level for TRRS.
My recommendation:
1.5mm top
3mm spacer (TRRS access)
1.5mm mounting plate (TRRS & USB access)
3mm spacer (TRRS & USB access)
3mm/1.5mm spacer (TRRS & USB access) -- 1.5mm might be tight fit, chances of shorting, no space for insulating liner.
3mm spacer
1.5mm base