I think that's mainly to cover their backs. There's no real technical reason not to do it, but numptys could connect what they think is 5V only to find it's unregulated and actually much higher.
It's perfectly safe to apply a properly regulated 5V supply to the 5V pin. You might like to add a diode between 5V and Vin (anode to 5V, cathode to Vin) to allow any reverse voltage to safely bypass the onboard 5V regulator, just to protect it from damage in case you should apply any load to Vin.