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What sort of documentation are you searching for? Are you looking for general information or something specific enough that you could write code based on it?
I don't know of any online documentation on this. Perhaps someone else will link to some. In the mean time here is some general information.
Magazines with the ability to switch between article text and page images can be in either MOBI or KFX format. The magazine you see in the Kindle for iOS app is likely delivered in KFX format. If you download the same magazine from Amazon's website using "Download & transfer via USB" you will get it in MOBI format. Both accomplish the same thing but use different methods to achieve it. I will describe the MOBI version since that is what you have examined already.
MOBI is a proprietary binary format. Kindleunpack attempts to create standard EPUB files that correspond to the content of MOBI file. There are some things that it does not currently handle and the special fields used in periodicals is one of them.
In the MOBI file the index structure that corresponds to the NCX has additional fields that kindleunpack ignores and so they do not appear in the recreated NCX that it produces. In the NCX file produced from your magazine you will see a list of entries labeled with page numbers that link to content in the HTML file of the book. Missing from that, but present in the MOBI file, are also links to the full size image and thumbnail image of each page.
Some magazines have even more detailed information, indicating which rectangles on which each page correspond to the content contained in articles.
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