A) Hi Clark, yes I recall there was an issue with the full swing vs low power with the ATmega644p/ATmega1284p the oscillator was interfering with the serial port in full power mode, it made for interesting times trying to use a serial bootloader.
that said changing the fuse bits in the NANO is very easy with the ATMEL ISP programer, step 1) make a backup copy of the firmware, eeprom, and fuse settings. 2) update the fuse settings from their current state to place the device in low power clock mode. 3) verify firmware, eeprom, and new fuse settings.
B) Jerry, did you run the numbers for other common catalog crystal frequencies? for example, would running the AVR at 11.052MHz and leaving the IF at 12MHz be a viable option?
P.S. Ashhar as an option could a person order the Randino with the NANO uninstalled? some people including myself need the real FTDI USB chip, the other types cause unresolvable usability problems. the drivers for the chip provided in my kit rendered my Macintosh unusable, I had to use a 3rd party keyboard and mouse to recover the settings.