Furthermore on iTunes, Apple took the decision in the past to incorporate all sync functions into iTunes and I think this is kind of weird. Apple did this because she thought this was convenient, because there was just one app to manage all kind of media (music, video's, podcasts, ebooks, etc.)
What Apple should have done is create a standalone Sync app and 5 standalone dedicated apps for music (iTunes), podcasts, video, books (iBooks) and apps. Those 5 standalone apps would be specifically crafted to access / play the media type and would have access only to the dedicated store. This way media could be managed by the user in the standalone app by media type and synced with the standalone Sync app that would do nothing else than just syncing the media between Mac and iOS devices. This is something users would understand.
But how can Apple explain her users now that ebooks from the standalone iBooks application can only be synced to your iOS device from an app that was created for playing music (iTunes)? Where's the logic in this?
In conclusion, Apple is not consistent and what once was "one app to serve them all" (iTunes) is starting to desintegrate in standalone apps (like iBooks) while syncing still remains in the motherapp (iTunes) which is kind of stupid, so Apple fix that!