I agree, this is an issue. I just don't know why Apple didn't get Samsung to provide the chips for the 6S and TSMC to provide for the 6S Plus, or the other way about. Considering they are different chips. So in short they are not the both the A9 chip, they may be effectively the same chip, but it seems obvious that they are different sizes and drain different power, so to me they are the A9a and A9b.
Personally, I don't have an iPhone 6S or 6SPlus, but I would be very unhappy if I had the Samsung version.
It doesn't matter if there is just a 2-3% difference or not...there is now a public knowledge that you can get 2 different chips inside the phones and one "it seems" is inferior to the other.
I also am not impressed by the claims "in normal use". I'm sorry, but everybody uses their phones differently. I know how much it drains the system by using VLC or playing Vainglory and going by reports, heavy CPU-based tasks could show huge difference in heat and battery consumption. I use my phone for watching videos using VLC and play power intensive games, so should I expect up to 2 hours less battery with a Samsung-based 6s compared to the TSMC version?
Anyway, I won't be upgrading until May next year, and I would like to think that Appl have sorted out this mess and just go with TSMC chips in their phones by then.