"Supplying voltage via the 5V or 3.3V pins [...]" to what?

fungus:

MarkT:
The Uno and Mega have power-switching circuits that detect Vin
and switch over to USB only if Vin is low.

That's the case we're talking about.

When Vin is low the 5V from USB goes directly to the output of the 5V regulator.

The regulator has no input, the output is connected to 5V. Every Arduino in the world that's running on USB power is doing that as we speak.

It's the word 'directly' that I sought to correct. Also the power management for an arduino board has some history. The very first design had no 'auto voltage switching' but rather the user had to move a jumper clip to choose from using USB voltage or on-board voltage regulator. Then they went with the current design but with an older different model 5 volt regulator. It was only after the (I think Uno rev1 board) change to a different model 5 volt regulator did a few people report damage to the on-board voltage regulator when they applied an external regulated +5vdc to the 5V pin. This lead to speculation that the new voltage regulator was more vulnerable to having external voltage applied to it's output. It seemed to happen to enough people that only then did the Arduino product page add the recommendation to not apply external voltage to the 5V pin. Most all linear regulator datasheets caution against this practice and many recommend in their datasheet to adding a protection diode across the input and output pins of the regulator.to protect the regulator.

So that's the history, somewhat unclear what advice to give at times. Obviously the Arduino company is taking the most conservative stand by recommending to not apply external regulated +5vdc to the 5V pin, but so many of us do it all the time, one way or another. I apply +5vdc to the board via it's ICSP connector pins when I burn bootloaders or upload sketches using programmer option.

However if I had my way and was designing a board I would eliminate the whole auto voltage selection function and revert back to using manual jumper clips.

Lefty