Hi,
I have forked the plugin here to work in reader mode as well (the plugin there currently only words in reader mode)
https://github.com/LizzardKing94/obsidian-note-annotations
90% of the stuff works I just need some help with the logic for changing the highlighted text colour, also the 'create new note' function in the popover window doesnt work. If someone could check the code's integrity, make sure everything is doing well. And also address the issue with colour changes and the 'new note' thing, i think it will all be ready. You can already compile and use it for yourself :)
Only tested on MacOS atm.