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It does seem like an odd duplication of information. I don't know why it exists either.
In response to the thread title, "Page number data in files other than apnx", page numbers for books in KFX format do not use an APNX file at all. KFX instead uses a data structure similar to an EPUB 2 NCX pageList. This is included within KFX format instead of as a separate file.
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