People switching back and forth between Macs and iPhones or iPads initially found it very inconvenient/frustrating to have window scrolling on a touchpad and content scrolling on a touchscreen.
It was decided that switching the Mac to be consistent with iOS would cause momentary frustration for Mac users (it requires a few days of retraining to get used to) but would be less frustrating for most users than preserving two inconsistent behaviors into perpetuity.
The option to keep the Mac on window scrolling was included to mollify those few Mac users unwilling to spend a few days or weeks re-training themselves to a reversed gesture.