I could see that working, but then the problem becomes constant panning and zooming to alternate between reading and annotating. Also, there's still the problem of keeping annotations in the right place with respect to reflowable text. This isn't really an issue for PDF, which usually have a fixed layout, but it is an issue for epub.

If the journal could be displayed alongside text, and synced up, that would be neat, too. This is an issue of the annotations consume a lot more vertical space than the text. If the annotations are linked to specific parts of the text, then when a piece of text is selected, the corresponding annotation is displayed beside it. That might require scrolling the journal differently from the text itself.

Also, consider going back and annotating some text between two previously annotated chunks. If the annotations are separate from the text, but anchored in it, then it becomes easy to insert a new one.

(Also, Dr T-- where in MD are you? It's my home state.)