well.. both ibooks and kobo are coded according to apple's specifications (with ibooks being from apple). i wouldn't expect either of them to recognize files that are installed outside approved methods.
if you take a look at the ibooks data in /private/var/mobile/Media/Books you'll see how the books are organized, and the Books.plist file contains all record information to organization of the book directories. I'm guessing iTunes generates this file when books are synced into ibooks, and iBooks when you download a file from Apple's store. If there was some way to trick it into regenerating the file on-demand you might have more luck.
maybe some jailbreak developer will come up with a way to load books on-device. actually would be nice if you could download .epub files through safari and have them side-loaded into ibooks.
for anyone who's curious, he's an entry from the .plist file
Code:
<dict>
<key>Name</key><string>The Art of Racing in the Rain</string>
<key>Artist</key><string>Garth Stein</string>
<key>Album</key><string>The Art of Racing in the Rain</string>
<key>Genre</key><string>Fiction</string>
<key>Sort Name</key><string>Art of Racing in the Rain</string>
<key>Sort Artist</key><string>Garth Stein</string>
<key>Sort Album</key><string>Art of Racing in the Rain</string>
<key>Persistent ID</key><string>FFB4236D6D14A6CE</string>
<key>Has Artwork</key><true/>
<key>Release Date</key><date>2008-04-01T12:00:00Z</date>
<key>Path</key><string>LJER.epub</string>
</dict>
this also exposes the ugly limitations of iTunes for managing books, the title of the book is referred to Album and author is Artist (just as it is in iTunes). Apple really needs to give iTunes an overhaul.