I bent up the VCC and AVCC pins, chopped traces on cathode (5V) side of D2 and the 10k resistor, and soldered wires to all of them to connect to an external 5V supply. This supply has common ground with the Arduino. I did this to keep the ATMega always on from a low-power regulator.
I believe this is safe as long as the rest of the board is always powered up before any ATMega pins are de-tri-stated. I've removed the bootloader (using ISP instead) so programming doesn't violate this.
What I do wonder about is the connection from RESET to pin 13 of the ATMega16U2 via a 10k ohm and capacitor C5. I think between the 10k resistor and C5 which should block the DC to the un-powered ATMega16U2 any momentary hit to that pin should be absorbed by it's protection diodes without a problem. Is that true?