They designed a CPU with such a single core performance that can’t be sustained by the thin batteries they installed in the problematic phones. That is why they introduced the power efficient cores with iPhone 7.
If that's true, then why was the battery replacement program and complaints about auto shutdowns largely confined to a limited serial number range of 6S phones? You provided a link to that exact program earlier, so I'm not following why you would believe it's actually a general design flaw.
I do think it's believable that the 6/6S processor design had a ratio between processing power and power efficiency that may not have been as ideal as other A series designs, but that's more about chip development not always being exactly the same from generation to generation in terms of improvement.