PWM commutation strategy for Sensorless BLDC
In your schematic, there is no theoretical advantage to either approach.  @Brian Drummond makes good points about it being easier to switch the low side, because the gates of these transistors are always at referenced to ground level, while the high side gates voltage must follow the motor phase voltage.  

Many controllers with a high side charge pump only charge the capacitor when the gate voltage is low, so the capacitor's voltage can droop at low speeds and provide insufficient voltage to drive the high side gate.  Keeping the high side switch "on" (using PWM strategy 2) for long periods at low motor speed will then cause the switch to drop out.

So, as in many cases, you make a design decision.  You can commutate the low side if you know your speed range and use a big enough charge pump capacitor and charging diode, and you can let the freewheeling body diode to handle the high side complimentary PWM commutation - simple circuitry.  If you commutate on the high side (or high side and complementary low side - if you don't want to rely on the body diode) you have to get more complicated, but at low speeds, since you will presumably be commutating anyway, your charge pump will always be happy.