See http://batteryuniversity.com/learn/article/how_to_prolong_lithium_based_batterie s
The fact that a SMART standard lithium battery cannot be drained fully because the device shuts off is a function of the international standards on certified SMART technology, not anything special that Apple does. Lithium cells become dangerous to recharge if fully depleted and may swell, burst or overheat and burn.
It is also well known that to maximize the useful life span of a lithium battery, it is optimal to avoid deep cycles (not full discharge, but simple depletion to a charge state well below 50%) and instead charge or partially charge more frequently to cause more shallow discharge/charge cycles. Doing that will significantly extend the useful life of the battery versus frequent deep cycles.
So draining the battery to device auto-shut off does nothing useful at all, with the current state of the capacity tracking software, and it will serve to cause the battery to age more rapidly than it otherwise would If it was just charged or partially charged well before auto-shut down occurred.