I just sent customer care a long message detailing my woes. This is to me the most telling part of the syncing experience:
It seems like when using cloud syncing you absolutely cannot keep a book "open" in the Kobo iPhone app. When doing so, no sync occurs when re-opening the iPhone app, and if you return to the home/library screen and try to sync to retrieve the bookmark saved on your other device, you cannot, because the iPhone has already overwritten the bookmark saved by the other device. The cloud bookmarking system seems very error-prone and there is a lot of stepping on toes going on in my testing. Perhaps when re-opening the iPhone app a sync could be performed, and a popup could be used just like on the Kobo Touch, asking the user if they want to update to the new bookmark position.
I don't know if this aspect of syncing is any better on other devices (i.e. Android), but this is just awful. If I have to think about it, it's not cloud syncing, it's hair pulling.