That boxed implementation was Apple's choice. Certainly, the company could have done things differently--it could, for example, have opted to stretch unoptimized apps vertically or to algorithmically resize elements. But it strikes me that Apple's decision to center non-updated apps on the iPhone's screen was not made with the user's immediate interest in mind. Instead, Apple's decision is one that only benefits users in the long-term.

My concern before I ever held the iPhone 5 was that, by centering older apps on the screen, Apple would render my muscle memory mostly useless: The keyboard would appear too high, off the bottom edge of the screen. Topmost tap targets would similarly appear lower on the iPhone 5 than they would on an older device, relative to the top of each device's screen.

Early reviews of the iPhone 5 confirmed my fears. :

The letterbox mode for not-yet-updated-for-the-new-display apps kind of sucks. It's not so much that it looks bad (my review unit is white; I'd wager money that the letterboxing is almost hard to notice visually on the black ones), but that it really throws me off while typing. My muscle memory knows where the keys are supposed to be relative to the bottom of the phone; letterboxing moves them all a row higher.