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

Yep. USB power goes directly to the internal 5V rail (and therefore to the output of the 5V regulator NCP1 1 17ST50T3G)

Nope, not directly, but rather the USB voltage first goes to a 500 ma thermofuse and then onto a MOSFET that is under control of the infamous arduino auto voltage switching function. If Vin has greater then proper minimum voltage then the board's 5V bus comes from only the on-board voltage regulator even if the USB is plugged into a PC.