I don't agree that 2 sizes of iPhone is any different from 2 sizes of laptop or two sizes of iPad.
Now, things are bundled together. If you choose an iPhone screen size first, you're implicitly choosing camera quality, materials, speed, fingerprint recognition, and such things all at once. If you like a plastic case (some people do!) then 4" is your only choice. If you want the best camera, you have to get a 5.5" phone even if that doesn't fit in your pocket. If you're buying a MacBook, you have to optimize ports, weight, speed, fancy new haptic trackpad, and other such things all at once.
Compared to other manufacturers, Apple is still doing pretty well here. But it's still considerably worse than it used to be.
For example, the difference in camera quality between the iPhone 6 and 6+ is minimal. Yes, if you are obsessed with 'the best' camera quality but want it in a smaller phone, you are faced with a compromise, but for almost everyone the phone size massively overshadows the trivial difference in camera. So people will pick the size they want and those who pick the bigger device will have the minor bonus of a marginally better camera.
Almost nobody obsesses over the full matrix of possible tradeoff the way you are implying. They just choose from what is available based on what is most important to them. The iPhone lineup is easy to select from based on this approach.
Yes, they could make things more orthogonal by say, not having the plastic phone, but it seems to me that this would have almost no effect of the ease of choosing, while just serving fewer customers.
