Thanks for all the feedback guys!
For the CP artwork, I'd try to mimic the design of the NES gamepad as much as possible. Each button has a white square with slightly rounded corners around it, for example.
The CPO does mirror the NES controller. However, arcade buttons are rather large, and I do not want to have too much space between them (=uncomfortable). As such I decided to place them all in a single rectangle.
Regarding the CPO ... Those black blocks just look too chunky. I would just use the stripes or, better still, don't do a CPO at all. The cab already looks very good without one.
The CPO was already printed and waiting to be applied
It should still be possible to cut a groove 3 mm wide / 3 mm deep. The plexi only needs a space to rest on, 3 mm should be sturdy enough to hold it.
The cab was designed for a bezel+plexi thickness of 9mm. Just using the bezel leaves a 3mm gap at the top and bottom, so I would need to remake the bezel from 9mm MDF. I decided to go with clear plexi: ordered and waiting for delivery. If that does not work out, than I'll go with your suggestion, and remake the bezel.
I also did some work on the CP
Note that the USB ports are not screwed in place yet as I cannot find a shop that sells black screws