I still can't bring myself to pull the trigger on a panel of crazy clocks. But in the meantime, I have decided to go ahead with a jig for at least single boards.
The concept is that the two ISP footprints are connected together, the two battery footprints are connected together and the clock footprint is connected to two inverse parallel LEDs. The battery, clock and ISP footprints that match up with the actual board will be populated with pogo pins. The extra battery jack will connect to a right-angle 1x2 header and the extra ISP footprint will connect to a right-angle 2x3 header. That will form the bottom board of the jig. The top board will have the two SMD LEDs mounted. The pogo pins will project out of the top, and there will be some rubber feet for stability on the bottom.
To use it, you connect an AVR programmer configured for a self-powered target to the 2x3 header and a single AA battery to the battery connector. You then hold a freshly manufactured board on top of the pins and press down (for hands-free operation, you could use a few ounces of weight - say a paperweight wrapped in electrical tape). You then use your other hand and press return on the Raspberry Pi that has the AVRDUDE operations scripted. If the programming steps work (and if the programmer is configured to not deliver target power), then that confirms that the boost converter works. At the end of programming, the two LEDs should start blinking in the correct sequence for the firmware that was loaded. That confirms that the firmware works and that the series resistors and flyback diodes aren't wired incorrectly.