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

retrolefty:
It's the word 'directly' that I sought to correct.

OK, it's not "direct" if we're being pedantic, it goes through a fuse and a MOSFET as part of the voltage selection circuit (directly above where it says "Rev3" in the schematic).

Electrically though, it's the same thing. The output of that MOSFET feeds directly into the 5V rail, and therefore the output of the 5V regulator.

retrolefty:
a few people report damage to the on-board voltage regulator when they applied an external regulated +5vdc to the 5V pin

The Arduino Uno Rev1 seems to use the same power switching circuit:

I don't see how connecting a 5V supply to the 5V pin is any different from using USB power.