I'll chime in here since I've designed quite a few plexi cases at this stage:
1: Decide on a clearance between the case and boards and work around that. 11mm is what I start at, most parts will clear 14mm easily and it gives you a bit more breathing room for displays
2: Decide if you want windows for displays. I personally dont like the displays exposed and always put a window in front. This also means that you need a fair amount of space between the panel and PCB, a cutout, or a thin display. In this case, going to a 20x2 OLED seems to make the most sense to match the little ones..
3: Case colors: Personally, I dont like the clear/tint plexi since it just gets covered in finger prints instantly. The matte black is my go to but you really have to fill in the engraving which can be tricky. There are a couple of threads about the techniques people use to do it.
4: with matte black, dealing with the LED rings can be done in two different ways imo: cut holes for all the LEDs and just stick them through the top panel or you can just make a clear round piece that snaps in like a display window with a hole in the middle for the encoder shaft (or a u shaped on for that matter, keep the middle black)
100% agree on the CV/gate jacks not being on the "brain", a D connector to a breakout box is the way to do it even if it's only a foot of cable connecting the two.
One other thing I dont think anyone has touched upon is the real estate that the core, aout, and any other related boards will take up behind the CS.