The diode in the RBBB is on the +5 supply. It provides the reverse-polarity protection if you don't use the on-board regulator, and plug in an external 5V, instead.
No damage "so far" doesn't mean "so good": I once connected a 12V LED array (one of those 1-inch "super jumbos" with 6 LEDs in series) into the lighter socket of my pickup, just to see how long it would last. It worked fine for about 3 weeks, then just quietly died, with no release of magic smoke or similar dramatic symptoms.
The AVR chip should already have protection diodes on all its digital inputs. If you're worried about spikes, you can probably get away with just putting a resistor in series with the input, so most of the energy will be dissipated there, instead of in the diodes (where there might be enough to blow one up, since they're tiny little things). You need the more elaborate protection on the power supply because it's supposed to let lots of energy through to run the system, so you can't just throw most of it away.
Ran