Originally Posted by nogle
Part of the difference is that KEPUBs are not EPUBs . I think that the book is delivered as a series of files rather than one file. This is probably what allows the features you like.
Actually, Kepubs are Kobo Epubs. They are not Adobe Epubs. Epub is a standard and Kepubs are fully compliant. The "wrapper" determines particulars regarding how the files behave and display. The DRM is different, as well.
When you adjust the book files now, keep in mind that you may need or wish to return them to their original form later on.