An Apple spokesperson gave us the following statement:
With the Apple-designed A9 chip in your iPhone 6s or iPhone 6s Plus, you are getting the most advanced smartphone chip in the world. Every chip we ship meets Apple's highest standards for providing incredible performance and deliver great battery life, regardless of iPhone 6s capacity, color, or model.
Certain manufactured lab tests which run the processors with a continuous heavy workload until the battery depletes are not representative of real-world usage, since they spend an unrealistic amount of time at the highest CPU performance state. It's a misleading way to measure real-world battery life. Our testing and customer data show the actual battery life of the iPhone 6s and iPhone 6s Plus, even taking into account variable component differences, vary within just 2-3% of each other.
That two to three percent difference seems to be quite a bit less than what others have experienced in their testing, but Apple's also working with a lot more data on how its devices perform than anyone else out there. For its part, Apple believes that regardless of who made the A9 chip in your iPhone 6s, you should get battery life in line with what the company claims -- and if you don't, chances are good the company will simply swap out your phone for a new one.