The only difference is that anyone who wants to reprogram must have an ISP programmer of some kind instead of just straight USB. That's not a big deal I suspect.
Back onto the topic of Dave's gadget, there is a cheaper solution if you already have an Arduino. The Arduino development board itself (various flavours) can itself be used as an ISP programmer. There is a whole page devoted to this subject:
http://arduino.cc/en/Tutorial/ArduinoISPOne presumes that "the Arduino crowd" (as someone called them) would have an Arduino. So basically you just upload the "ISP sketch" to your Arduino, connect up 6 wires to the ICSP header of your target device (reset, power, Gnd, MISO, MOSI, SCK) and then upload your sketch in the usual way, telling the IDE that your "programmer" is the "Arduino as ISP".
So, a "free" programmer, if you need one.
The whole power supply project is a cool and educational idea. My next test is going to be to try to read back the voltage on the power supply using the analog input (ADC converter) on the Atmega, so that I could test if, when requesting 5V output, I actually get 5V. Presumably, once calibrated, this could be used to see if current limiting had kicked in. I'm guessing that Dave's design does just that, since there are lots of ports available on the processor chip for this sort of thing.