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In theory, you can add the apnx file to the book record and the Kindle driver could be modified to check for the existence of an apnx and use it when present, but this is something that I think is rather fragile, so I'm not really motivated to implement it. For example, if you decide to do a mobi-mobi conversion, what happens to the apnx? The information in the apnx will no longer co-incide with the structure of the MOBI. And then there will be problems if amazon decide to change the format of the apnx file, like they did with the mbp file a couple of years ago, which broke fetching annotation from newer Kindles.
Incidentally, there's nothing "pseudo" about the apnx file generated by the plugin. It simply uses an algorithm to calculate the number of pages in a book.
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