One thing I can tell you for sure is that if anything else is connected to the SPI lines, it cannot program the AVR saying the AVR doesn't respond, so that's why I've been assuming that it uses SPI to program OTA.
I know this because I am using SPI as master from the AVR to control other peripherals (I take the lines from the ICSP connector) and I have had to add circuitry and logic to isolate the SPI lines when I need to program the AVR via OTA.