One is probably already running hotter than the other one!So one will run hotter, slightly, than the other and thus will probably throttle first.(reducing clocks) As a result battery life shouldn't be effected, but I could be wrong.
Apple definitely designed redundancy into their hardware to account for this difference. I wouldn't worry about it.
http://www.technobuffalo.com/2015/09/27/iphone-6s-overheating-for-some-disabling-led-flash/
"FOR SOME"—i.e. for those with the "TSMC version" of the iPhone 6s/6s Plus?