You've identified the primary reason that I have ONE title on my iBooks, and DOZENS on my Kindle app. With Kindle, I can sync between multiple iPods, iPad & on my Macs, AND I can even access those title cross-platform if needed. AND, Kindle will keep my locations synced across those devices.
There's not many things Amazon does better than Apple, IMO, but Kindle truly dwarfs iBooks in my mind.