I don't think it would be difficult to deal with that hard case at the user end. Rather than writing "What does this word mean", you could write "what does 'EEE' mean". If that note is at the bottom of the page and 'EEE' isn't there, I would figure it has to be at the top of the next page. That would be a minor annoyance, but nothing compared to having to pretend you're a Buddhist monk writing on a grain of rice, which is my current workaround for the zoom/annotation debacles.