You're correct - the layout is a feature within Amazon's implementation of the AZW/MOBI format, currently only on the Kindle.
I'm hoping that Amazon decides to implement it on their 'Kindle for iPad' app. The issue might be legal rather than technical. Amazon's contracts with subscription content providers might be only for the Kindle hardware.
It would be possible to mimic the layout in an ePub that would display on iBooks with some effort, but the key element would be mimicking the joystick navigation for next article/next section. For example, if a one-finger swipe means 'next page', then perhaps a two-finger swipe means 'next article'. That would need to be implemented within iBooks. If you do email Apple, you might generalize the request to include the notion of a two-finger swipe for 'next chapter' within a book as well.
G
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