Just to simplify what Geoff said: If you use the KOBO desktop app, it will download a kepub only. If you use a KOBO device to DIRECTLY download the book, it will download a kepub only. To get a regular epub (if available) you MUST use the download link from the website AND Adobe Digital Editions (ADE) if it has DRM or just the download link from the website if it has no DRM. For non-DRM books you can download direct to the reader via the browser on the reader (works for some sites anyway, not sure if that works direct from Kobo because I've never tried it).
As Geoff said, even if you do download the kepub, you can also download the regular epub (if available) as well. I mostly read kepub versions downloaded direct to my Kobo, but I do download and de-DRM my books as regular epub for backup purposes.
Last edited by robko; 02-22-2014 at 11:57 AM.