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ePub's use a completely different rendering engine than kePub's on Kobo devices (Adobe's RMSDK instead of Kobo's Access).
The page numbering thing has to do with the way each engine handles such things. In the Access renderer one page equals one screen. With the RMSDK pages can be handled two ways. If the ePub has a page map then the pages can be mapped to page numbers in a print edition of the book. In the absence of a page map it assumes that every 1024 bytes is a page. Either way a "page" in an RMSDK rendered book can be, and usually is, multiple screens on a device depending on screen size, font size, line spacing, etc.
NOTE: There are others here more well versed in this and some of my info may not be exact.
The spacing at the bottom of some pages with ePub's can be due to a few things IIRC (which I may not as I use sideloaded Calibre kePub's on my device for everything). One is the files widows & orphans setting and the other can have to do with the length of the paragraph. Like I said I might not be recalling this correctly, but someone will be along who is.
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