All my complaining about how Logos still missed the mark on notes was 'cause I was thinking down the wrong path. I was so intent on getting things attached where they belonged that I forgot to consider general notes and my content as a combination. True, I'll need to run a Passage Guide to see what I've already build notes for but I can build a Passage Guide with nothing but my content.
Now we just need to resolve the collapse/expand a note need which I don't think Logos hid under "my misthinking"