I am wondering whether the caution added for the Uno R3 was really to protect the voltage regulator. Here's what ON Semiconductor says about this:
Protection Diodes
The NCP1117 family has two internal low impedance diode paths that normally do not require protection when
used in the typical regulator applications. The first path connects between Vout and Vin, and it can withstand a peak
surge current of about 15 A. Normal cycling of Vin cannot generate a current surge of this magnitude. Only when Vin
is shorted or crowbarred to ground and Cout is greater than 50 F, it becomes possible for device damage to occur.
Under these conditions, diode D1 is required to protect the device.
Given that the VR input on the Arduino board should never go to ground, the built-in protection (15 AMP) seems to me more than adequate.
Perhaps the reason for not wanting you to attach power to the 5V pin is to protect the ATMEGA16 used in place of the USB-Serial converter used on older boards? If that's the case, your bypass diode cure is worse than the disease! Perhaps someone involved in Uno R3 development could chime in here.
The Nano doesn't use the Atmega16, and there's a blocking diode between the USB V+ and the 5V line. That's why the Nano's USB converter can't be powered from Vin, but just from the USB jack, but it also means that externally-supplied power at the 5V pin can't in any way damage it. TI's data sheet for the UA78M05 makes absolutely no mention of reverse current flow problems. In other words, for the Nano while a bypass diode probably won't cause any harm, it just doesn't seem to serve any purpose either.
Ciao,
Lenny