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On a Kobo ereader, ePubs use the Adobe Synthetic Page Number algorithm which is consistent regardless of font size, margins, etc. while the kepub algorithm is pretty much one page per screen so any changes in font size, margins, paragraph spacing, etc. will affect the page count.
As for the starting in the middle of the book? The only times I've seen that is when the navigation document (nav.xhtml for ePub3 or toc.ncx for ePub2) is not correctly structured.
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