Excellent thread idea! I am surprised it's not been posted before. I'm sending the link to this onto the development team.
Speaking to the Sync side of things, try the next version (should be available this week) and see how that works for you. We've made a couple of changes.
One is to how the book progress is calculated, so that should be far more accurate than it was.
The other relates to the actual position within the book, what we term "cloud bookmarking".
Over the past few releases we have made a couple of changes to this, as there were a few issues, one of the big ones being that we were not correctly saving the position you were at. If you used one device and you did not sign out of your account, then you would probably would not have noticed, as we store the position locally and also sync it to the cloud.
If you used more than one device you may well have noticed when you read the book on one iOS device and then went to another device and opened the book, it would not be in the same position. As said, this was previously fixed.
The soon-to-be-released version has another fix relating to cloud bookmarks, specifically how we were calculating where in the book you were. What happened was that we would not get the position reference sent back to us and this caused us not to be able to send a cloud bookmark to the server, and thus when you opened the book on another device, you would not be at the correct position in the book.
At present, I know of only one existing issue with cloud bookmarking; If a book does not contain, or does not correctly define the tags we use for cloud bookmarking then a bookmark will not be sent to the server and therefore you may find on other devices that you are not in the correct position in the book. This is a pretty rare situation and it would be a per-book issue, so if you find a book where it's not working, do let us know and we will look into it.