Take a look at the datasheet, it talks about different methods for powering the thing if I remember correctly. Various voltages, powered from USB, powered from external source, etc.
I did scan the datasheet and I couldn't find anything that said the USB portion of the chip operated differently when the chip was run at different voltages. Again, I was just searching on USB through the datasheet, I didn't read the whole thing as the actual datasheet is 300 pages long. Just soliciting an expert opinion here. I guess if the USB doesn't end up working I can still use the board via the programming port.