With a new design for a 3D printed/printable case, I'm going to ditch the long-shaft buttons and go with normal ones. There will be a button extension that will sit in the back of the case between the actual switch and the back panel. This should make life much easier for my assembler.
In playing with rastered LED matrices in other contexts, I've learned that ghosting can be sometimes caused by the internal LED capacitance self-powering the LEDs after the raster on-period has ended. The workaround for this is resistors from the anode(s) to ground. I've added at least footprints for these to the board, though whether they'll be universally populated or not remains undecided.
Lastly, I've ordered a board with footprints for non-right-angle through-hole antenna and power connectors. Going this way would allow the antenna and power to come into the back rather than the sides. Some validation with a case design will be needed to decide whether or not this will be the way forward, but it's at least worth an experiment or two.