I finally got in some parts I had been waiting for from digikey, and was able to throw together a little hand-wired prototype using the new cluster design. I was able to verify there's no light leakage problems between the different keys, and all keys were causing a high enough voltage swing on the phototransistor to trigger a high logic level.
I also realized I had been carrying over the assumption from the previous design that everything would be driven at 5V. But the ESP32's input pins aren't 5V tolerant, so I'll need to switch everything to 3.3V. So I swapped out the LED resistors for a lower value to maintain the same current, and verified again that there's enough of a voltage swing at 3.3V for all the keys.
Incidentally, all those 22g solid copper wires don't make a half-bad mount for the cluster. It's not quite stiff enough, but maybe if the wires were shorter or a bigger gauge. That might be an idea to explore in the future, for a different type of adjustable mount.