Regarding bad/misconfigured nvram values... It would make sense for the bootloader to check whether or not the nvram reset button is pressed before configuring the clocks. That way, should a bad setting be entered, sane defaults would be applied at power-up.
Well, ASUS guys decided not to wire JTAG out of the chip except TCK line... So, playing with CFE is very dangerous, especially at the early stage...