Hey Forrest,
a quick look at the Onefinity Controller Schematics (rev5) shows: The Raspberry Pi exchanges data with the AVR ATXMEGA192A3U (datasheet) only via I²C Bus (SDA/GPIO2 (pin 3) and SDC/GPIO3 (pin 5)) and over the serial interface (TXD/GPIO14 (pin 8), RXD/GPIO15 (pin 10) and CTS/GPIO16 (pin 36 of Raspberry Pi GPIO header)). Note that there is also a TinyAVR microcontroller on the board which measures and controls current that is connected to the same I²2 bus than the main AVR. That’s all.
The remaining connections between the Raspberry Pi and the Onefinity AVR Mainboard are +5 V, GND, RESET and since revision 5 of the board, you have pin 40 of the GPIO used as SHUTDOWN for the new little circuitry that allows the Onefinity Controller to power itself off by itself (what a Raspberry Pi is unable to otherwise)