True though that may be, I think some people only want to buy the flagships because they can be assured of a certain level of quality (no shovelware, to start with) without having to go through hoops installing/uninstalling this or that, or potentially void the warranty with custom ROMs.
For those people, the alternative Android offerings just aren't on the radar.
And last but not least: timely security upgrades (many years into the future)
I'm most definitely not an Apple fan, but the thing they have is every phone is quality. You don't need to wait six months after the device is released to see if the early adopters had major problems.
On the other hand, the apple ecosystem doesn't have fire sales like Android does, getting last year's hip kick-started flagship got $200-300 isn't so bad, even if you need to do it way more often. See Amazon fire phone, nextbit Robin, essential phone; these were all a great value when they went on sale, although the fire phone has no back button, so it was more terrible than the others, but also cheaper.
build quality issues are not widespread to the whole android ecosystem. apple kind of get the crown as long term phones because software support and hardware warranties, but it's not as to say that there are no android phones that can match them in half life.