Strangly I've been able to do that since mavericks was released. Problem I'm having though is in the same area. I can see all my books, comics, and pdfs under that section but the only way I can get them onto my iPhone is to select Sync Books at the top and then select Selected Books as the option and choose my books or pdfs etc. Its when I select Sync Books that the issue comes up, I get the following message.
Are you sure you want to remove existing music, movies, TV shows, books and tones form this iPhone and sync with this iTunes Library? Options are Cancel or Remove and Sync.
I manually manage my music and additional contect on my iPhone and don't randomly select music from my library. If I choose Remove and Sync it erases my music from my phone and removes the manually manage music option, but it also DOESN'T select sync music or any other sync options on the other sections. I can choose to do the syncs but it takes a lot longer and has less options of picking and choosing music then just doing it manually. If I select manage music manually again it removes the sync option from the books area.
Even more upsetting is if I sync the books and remove everything else from the phone then select manually update music and it removes the sync it leaves the books on the phone. I'm finding this lack of intagration between operating systems and programs very frustrating. It wasn't broken before and they add a nice feature with iBooks for Mavericks and they break what worked.
I spoke with technical support and they said there wasn't an issue you can email yourself your pdfs and save them to ibooks one by one and you can download books etc from that you purchased from the store again on your phone. Personally I prefer to save my music, videos, books, etc to a external hard drive so I have it when I want it and I don't need to worry about it disappearing from iTunes or the iBooks store.
If you find away to get books and pdfs on your iPhone that isn't a massive hassle let me know. I still don't understand why when you plug your iOS device in that iBooks doesn't open just like iPhoto does. You'd think you could just sync that way.