E.g., if I add a new page to a notebook and want that reflected in whatever cloud I’m using - as a user, I have to delete the previously uploaded file then manually upload the notebook.

If you have multiple notebooks or items to sync, you have to do it one by one.

EDIT: I'm not sure now -- I might experiment a bit with this to see if it'll save my notebooks from the device to other clouds. It looks like you can use it as a quick way to get PDFs to your device, but if you use it as a journal you are SOL.