The number of pages as dictated by the APNX file are not the same thing as the number of screens. In other words, turning the page on your Kindle does not equate with turning the page in a paper book. The page number transitions are linked to specific places in the book, so how many screen changes equal a page turn depends on font size and other factors.
Amazon originally introduced the page number feature because many people wanted a metric that was equivalent to what they were used to - paper books. The books from Amazon that have this use the print version of the book to determine where the page transitions go. Depending on the print version used, the amount of text per page can vary significantly from the amount of text displayed on your Kindle's screen.
When you use calibre, the APNX created is an approximation of this same function, with the difference being that it is not tied to an actual print version like Amazon's are. It's sort of a compromise for those who want page numbers.
I hope this made sense. I'm on my second cup of coffee.
