I don't thin their is a logic to shut off motors at any point. I agree with you, it's better to kill batteries rather ruining your P3. I feel if the batteries are drained off, they can't give enough current to keep P3 flying and if load on the motor is more than what it can take care off, motors tend to stall.
Also we need minimum voltage to sustain electronic system. We have just one battery in P3 to feed power to motors and to maintain electronics.
Battery voltage is flat up to certain low charge levels and then it rapidly droops down making everything unstable. Land your P3 sooner when you get low voltage warning. We always assume that warning level is correct. This could go wrong if the batteries were not calibrated.
I have seen many other varieties of LiPo batteries in the market they are intelligent to shutoff supply in case of critical charge level is reached. We don't need such batteries for flying. Hope P3 batteries do not have shut off mechanism.