I've finally gone and pushed some updates to the git repo. Demo 2, the one that's programmable over USB, was not in the repo until now; this is because I completely forgot I hadn't routed the PCB before I published the project! When I did start routing, I didn't find a way to connect all three LED channels, so I've elected to give it green-and-blue LED control only.
In addition, I've added a fourth demo, which uses two 555 BGA ICs instead of an ATtiny84A. This is thanks to some "Coulda used a 555" comments on the post that made the Hackaday blog. Sadly I couldn't get those boards in time to enter the 555 contest, but it's still worth a go I think.
I have a few ideas for how to address the short-circuit problems I encountered with the PCB I assembled previously. The obvious solution is to slap another flex PCB on top, which will create a double-sided USB connector. However, that would end up being about 0.85mm thick, which I worry would cause too much downward scraping force on the flex PCBs. There are vendors with thinner polyimide substrates, which I will look into.