@jojag This is solved with Sliding panes / Andy mode plugin as mentioned above by @pjeby. Ctrl+Click opens the note for editing in new pane adjacent to the current pane so you also see the current context and can drag things if you need to. With pop-up it would be hidden behind. Closing the pane takes focus back to originally focused pane and whole workspace is exactly as it was.
The pop-up being in rendered/preview mode allows to quickly verify that I am opening the correct note and also allows quick navigation by opening one pop-up from another and then automatically closing all.