So far as I can tell this still is not possible. I need the functionality so that I can write a note once and attach it to the 8-10 verses in the Bible to which it applies. However, I am willing to compromise. When I do a search on a word it comes up quite nicely as being in my notes. If the passage guide were to pick up the note based upon a citation within the note, the system would be quite functional - I'd even quit complaining about it not indicating that the note existed in the Bible pane.
But I still get to wonder what is so difficult about the paired-key table that you didn't provide for notes with a many-to-many relationship with a reference.