What is the optimal protection diode placement driving a relay
Putting a regular diode across the transistor (reverse biased) will do nothing of value in a low-side switch of an inductive load. The intrinsic body diode in a MOSFET is thus of no use in preventing breakdown. 

You can put a Zener diode across the transistor, of higher breakdown voltage than the supply, which may speed the relay drop-out (to the extent it allows the voltage to go higher than the supply), at the expense of being harder on the transistor during switching. You can also put a zener in series with a diode across the relay. Or a resistor in series with a diode across the relay. 

Whether across the relay or the switch is better is mostly a matter of how the currents and voltages change when the switch opens and closes, for EMI caused by the coil (usually not that much compared to the contacts).