My guess is that collection syncing only works with books purchased from iBook Store because Apple doesn't offer "iTunes Match" equivalent for iBooks, unlike Google that allows you to upload your books to their cloud and access them from any device.
And that's a shame if you ask me.
I'm still trying to figure that whole iBooks thing. So basically, once you open iBooks (for Mac) for the first time, every PDF and ebooks you have in iTunes gets transfer to the iBooks app... Afterward, when you get back to iTunes, you just lose your iBooks section on the iTunes sidebar... So you think that, from now on, you must use iBooks instead of iTunes to sync your (non-iTunes) books and PDF to your iOS devices. But no, as it turn out, you still need to use iTunes to do that... So now you have to open your PDF/ebooks with iBooks, then go back to iTunes, make sure your iOS device is registered and available, then go top the book tab, select your newly added PDF/ebooks and sync your device. And you do this for each iOS device... And you must do this every time you add a new PDF or (non-iTunes) ebook (if you choose not the sync your whole iBooks library).
Seems to me like quite a lots of steps to sync PDF and it's a bit counter-intuitive. Why can't I just "save" my PDF or (non-iTunes) ebooks on my iCloud directly form iBooks, like any TextEdit document for example? Then I could just open them from any iOS device and they would always be in-sync.
That wouldn't be a "magical" solution but it seems to me that it would be quicker and in some ways, more logical.
I can't even start thinking what will happen if they ever decide to take out the music and videos files from iTunes....