You hit the nail on the head, the battery either had manufacturing defect or was totally under specced by Apple. The fact they had to recall some of the 6s phones for battery issue makes me think the IOS tweak was to reduce the amount of phones needing recall, with any manufacturing process there will always be a slight variation, some batteries will perform better than others, Apple identified which would be worst performers and included them in recall, the others were handled by Apple introducing the throttling, Apple knew there would be a huge failure rate of the batteries within the 2 year warranty period so introduced throttling to hide it, they were hoping to hide the problem until the bulk of the phones were outside of warranty period. Look when the 6s was released, when the battery recall happened and when IOS was changed to bring in throttling. Apple hoped that people would not realise the phones had been slowed down.
https://en.wikipedia.org/wiki/IPhone_6S#Unexpected_battery_shutdowns