The Vin header pin is probably intended more to distribute raw power to shields
when the main board is powered from the power jack than for use to connect
input power to the main board. As noted, the difference between the 2 levels
is always 1 diode drop.
OTOH, and this comes up a number of times every week, using a high voltage
like 12V to power the board means the tiny surface-mount 5V regulator will likely
get hot if you draw more than a couple of hundred mA off of it.