Die size isn't everything. A better implemented 16 nm process could outperform an inferior 14 nm process. And that appears to be the actual case that we're seeing here. In fact when the news originally broke of the dual-sourced A9, people assumed the Samsung chip would be the superior option due to the better process on paper.
Ultimately there is significant variation in all chips due to the nature of production of the wafers and needing to have a reasonable yield. You can't reject every chip that doesn't come out with the best leakage and voltage. The real questions are ultimately:
A. Is the variance between the average TSMC and Samsung chip really significantly bigger than the expected variance we'd see between better and worse examples of a single sourced chip? It's also possible that TSMC's process simply has a tighter variance and that good Samsung chips are just as good (or better than, owing to the 14 nm process) as TSMC chips.
B. Are Apple's battery life claims based on a worst case scenario (e.g. a Samsung A9 that was on the lower end of passing QC)
C. How much does variance in the chip affect battery life versus variance in other key components like the LED backlight and the battery itself? It's quite possible that even with a less efficient example of the A9 you've still got good battery life since you "won the battery lottery" and or the "backlight lottery".
FWIW my IPhone 6S Plus has a Samsung chip according to the app script some dude posted to test it. But honestly my battery life has been superlative, so I likely got a better example of the battery and/or the backlight or whatever other components significantly affect battery life. Or maybe I just got one of the better examples of a Samsung chip. There are a TON of variables at play here; a modern smartphone is a complex device with a lot of components and basically every single component has significant variance due to manufacturing processes.
I also suspect 9.1 improves battery life a good bit (I've been running the beta from day 1 since my backup of my old phone was on 9.1 beta and i needed to upgrade to restore from that backup). 9.1 seems to be better optimized than 9.0, at least as far as performance goes, so I'd guess it probably does better for battery life as well.