If the inductor RMS current is 50A, then if using a freewheel diode (a normal one) would dissipate around 40W, that's a pretty high loss, taking into account it could be much lower. Using a schottky diode would decrease that loss to around 20W (1% of the maximum output power). Using the synchronous FET, that loss could reach around 15W without counting the rise/fall losses.
About using diodes, what frequency are your working at? If 2 diodes in parallel are faster than the single FET body diode, use the faster solution whenever the time transitions become a problem. If "speed" is not a matter here, use the one that will provide you a bigger safety margin. It will be better at long terms.
A synchronous boost will only improve efficiency. That can be seen in ultra low power or maximum efficiency circuits, where it can reach about 98%, and a diode could drag it to 90%. But as you are working with very high currents there's almost not big difference (in power loss) by using synch or freewheeling, so if I were you, to avoid complications, I'd choose the non-synchronous.