A way for iBooks to sync bookmarks via iCloud, not iTunes Store account?

My wife and I have our personal iCloud and iTunes Store accounts setup in a way that I thought Apple recommended:

- I have my own iCloud account for all email, sync, and backup features

- my wife has her own iCloud account for all email, sync, and backup features

- we share a third Apple ID for all iTunes and App Store purchases

However, we're starting to read more iBooks together, and we've found that iBooks syncs your bookmarks/notes/highlights between devices via the iTunes Store account, not the primary iCloud account (Apple's documentation also states this under Can I bookmark and save my page? http://support.apple.com/kb/HT5557).

Is there a way to get iBooks to sync this stuff via the device's primary iCloud account, not the iTunes Store account? Since everything else syncs via the iCloud account, could this just be an oversight in how iOS syncs things that Apple might fix soon? Or do we need to change the way we purchase all our apps, books, and media?

Thanks for any help.