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If you sideload the book in epub format, then the page numbering will be the static scheme as used by other Adobe based readers.
If you download the book directly from Kobo to your reader you will get the book in kepub format, which will be displayed with the dynamic per-chapter numbering scheme.
But there are two issues you might also consider:
First it is possile to convert the epub to kepub and sideload the kepub (with some limitations) in which case you get the per-chapter numbering scheme. However sideloading kepubs is not officially supported by Kobo, so there is no guarantee you will always be able to do this in the future.
Second, for books bought from Kobo you can download a kepub version directly from Kobo (not sideload it) but still manage the book with Calibre. You do this by downloading the epub version into Calibre, and Calibre will match it with the kepub version on the device. This allows you to change the metadata, send new covers, etc. for the book on the device by editing the record of the epub copy in Calibre.
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