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There's no guarantee that kindlebooks that were created with the intent to mirror a print version were mapped correctly. In most cases, it's not Amazon that's responsible for the apnx file anyway (other than providing/delivering). Kindlegen (locally or the KDP upload version) takes one of the two possible page-mapping schemes available to ebook makers and incorporates that data into one of the headers in the dual-format + source output of the kindle conversion process. On the retail end, an APNX file is then generated from that header info and passed onto the consumer (along with the correct format for their device/app).
The process may not be exactly the same for a big publisher, but the main point still holds: a human (and not very likely an Amazon human) is responsible for supplying the proper mapping to "real" page numbers. Some are probably satisfied with a quick and dirty approximation, and some take care to do it right.
I don't know if there's any quality control Amazon performs to ensure the mapping is accurate, but I doubt it. They probably rely on users pointing out discrepancies that they can then pass on to the publisher.
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