majenko:
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.
Yes several people have shared that view, including the addition of the diode across the on-board 5 vdc regulator. Also keep in mind that powering via the 5V pin also doesn't allow the arduino auto-voltage selection circuit to properly isolate the USB power from the board when you attach a PC to the USB connector for uploading and/or serial monitoring, as there is no Vin voltage to trigger the voltage switch which isolates the USB power from the board's 5 volt bus. Having USB 5 vdc and the external regulated 5 vdc voltage source effectively wired together is not considers a good engineering practice.