The books that you get from Kobo, and transfer to your device using the Kobo desktop app are injected directly into the SQlite database. With these books you get the chapter page counts only.
With regular ePubs you get the entire book page counts.
(At least this is what I remember from an older thread)
@PERTU: I believe the answer to your repeating page number thing is this; Someone at Adobe decided that the mobile software treats, lets say about 3000 characters, as a page ( no idea what the actual number is, not gonna waste my time counting). It uses that static number to generate the page numbers and total pages in a book. You'll notice the most annoying feature of this scheme is the little page numbers that the software draws OVER text on the very right hand side of a line where it considers a new page to start.
The number of times a certain page number will be repeated will usually be consistent, but when you're dealing with a string of pages that are light on text (say, conversation between characters without much narration), it'll take more pages to reach this stupid static number Adobe came up with.
here's the older thread about these annoying page markers:
https://www.mobileread.com/forums/showthread.php?t=83588