There is another advantage with the current position of Vin.
There are two ways to power the board from a battery : using the power-plug or going into Vin directly.
If you use the power-plug, the board is protected (by the diode) from hooking up the battery with reversed polarity which would kill the arduino.
But the diode will also eat up ~0.6V of the battery-supply voltage, thereby shortening the time the arduino will run. (The voltage-regulator needs a minimum input-voltage).
When you plug the battery into Vin directly, it will kill the board if you get the polarity wrong, but if you do it right the arduino will run significantly longer…