Page mapping in the Kindle for Mac app is dependent on two things. An encrypted question and answer between the app and https://kindle-app-services.amazon.com
. A value which appears to be a result of this exchange is written to ~/Library/Application Support/Kindle/storage/.kindle-info .
When I agree it writes it back to the file. The .kindle-info file appears to be a settings file with encrypted values.
At this point I can't see taking the time to look into this further as it's highly application specific and the APNX's work on the Kindle. This tells me that the files APNX's that are being generated are fine but Amazon is doing more within the app before it will use an APNX. Worst case when you open a book it checks with Amazon if it's one of theirs and will only load the APNX if this is the case. If this is the case then there isn't really any way around it.