As both @theducks and @ownedbycats said, the important thing is using the same method for all your books.
As for using a paper book as the reference, I have one pbook in a hardcover, trade paperback and paperback version. The page count varies from 396 to 478.
Since I read epubs, my preference is ADE. For a Kindle owner, APNX is likely the better choice. I looked at the various downloadable page counts and was not impressed by the consistency.
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