This response from Apple is actually completely predictable, and their explanation, likely written by their PR and lawyers, is not unreasonable.
There are many other components in the iPhone that drain the battery on regular daily use. So a test that turned almost everything off, and only stresses the A9 processor is not the most representative. I do buy that.
I guess it all comes down to how you use the iPhone. That extra few percents of battery power in theory could allow you to make one additional life-saving phone call. But I wonder how many owners actually use their iPhones down to 0% battery level regularly.