The more settings you have, the more inevitable this becomes... Assume for a moment that any given default you set, works well for 99% of your userbase. Then, the number of users satisfied with every last default breaks down as follows:
1 setting -> 99% of users satisfied 2 settings -> 98% of users satisfied 20 settings -> 81% of users satisfied 200 settings -> 13% of users satisfied
Apple has a lot of settings. Even if their defaults in general work for greater than 99% of their users, it becomes unrealistic at scale that every single default will satisfy any particular user, let alone all of them. Thus, those third-party apps that you see become popular in aggregate. That doesn't necessarily mean that Apple's defaults are wrong. They could be absolutely killing it on the defaults, and you would still expect to see these results -- in which case you would expect them to devote their attention to the common case, and to let the third-parties pick up the edge cases.
I suspect the same is true in the general case in the ios app store: that there is a long tail of apps used by a tiny %age of users, but with an enormous user base that's enough to make a free or even paid app.
And after about 35 years of mousing and about four years of iphoning I expected to want to revert apple's change to mouse-gesture-scrolling with Lion, but after only a few seconds I was sold. YMMV, of course, but I agree with the "99%" hypothesis.
The vast amount of MacOS apps built by the community to undo Apple's terrible and backwards UX choices, and the amounts of sales those apps get, disproves your theory that over 99% of people are fine with the defaults Apple forces on its users.