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I have a suggestion to improve the usefulness of notes in Logos. It is based on the ideas underpinning the 'interleave' package for EMACS which is influenced by Blumenbach's system of note taking. The basic idea is to enable a user to see their notes next to but separate from the text. The way I imagine this is similar to the 'Multi-Resources Display' functionality, except it is your notes next to the resource, as the block of text moves, the notes would also show and disappear in the adjacent column.
https://github.com/rudolfochrist/interleave
http://takingnotenow.blogspot.com/2008/07/note-keeping-in-1786-blumenbachs-system.html
If you can find a way to incorporate this into Logos, that would be extremely helpful.

Taking note: Note-keeping in 1786 - Blumenbach's System of Maps
takingnotenow.blogspot.com
— Edited
Thank you for posting this. I have just tried interleave mode for Emacs and I have to say that this will fix an immediate issue I had while taking notes on PDFs. Emacs never stops amazing me!- Thanks for the link to the Blumenbach article.