The page number algorithms don't have anything to do with conversion (directly at least) - they're actually applied when you transfer the ebook to your device. As to why you're seeing such a huge discrepancy I haven't a clue.
For sony the page count comes directly from the Sony device - which uses a in-built Adobe Digital Editions algorithm. The Kindle page count is supplied by Calibre though, and this is an algorithm reverse engineered from the Kindle behavior, so it's possible it won't always agree with Amazon.
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