Now, do the voltages of the Arduino board and the FDTI interface need to match? I understand that the "5V" board is clocked at 16MHz and therefore mightn't run properly when powered by a 3.3V interface. But is there anything wrong with programming a "3.3V" board with a 5V interface?
Isn't it the same ATmega168 chip on both 3.3V and 5V boards? The chip spec says it can run at 1.8 to 5.5V, although it needs lower clock speeds at lower voltages. So if I apply 5V to the Vcc pin of a 3.3V Pro-Mini board, it should be ok?