Vin is regulated down to 5V internally, everything else is strictly 5V. Vin is solely to allow powering from a source greater than 5V (well, greater than 6.5V actually). For instance you might have a 7.4V 2S LiPo power source - that could go to Vin.
The microcontroller pins will fry if exposed to voltages over 5.5V or less than -0.5V (powered up), or outside the range -0.5V to +0.5V when powered down.