iOS works the way it does to make money for Apple. First it was to appease carriers to enable the devices to exist. Then it was to appease publishers to get content on the devices. Now it's to make that sweet, sweet app store commission. That there are benefits for device owners who are willing to give up their freedom is a happy accident.
Note that every stage you have described has been called "security". Security is inherently a multi-perspective endeavour, and the word gets abused by powerful entities looking to preserve their own security, likely at the expense of your own (eg the TSA). I do agree that end users receive benefits from Apple's security, but to insist that explains the whole story is hopelessly ignorant.
I would argue that at least some of those holes were indeed imagined, that’s why iOS works the way it does and not the way parent would like.