Another option is to limit all your notes to the one paragraph/block. A new keyboard shortcut to add a sequential note, and a display set so that the notes appeared sequentially on screen in separate panes.
This is one reason why I suggested “document spanning” be added as a feature. If multiple short documents could be treated as one when editing (like Ulysses and Scrivener do) then the documents could be much shorter… (It would also allow the file manager to work as an outliner).