To round things off, I now have what I think is a nice integration.
For every project I (will) create a new DT database and a new Notebooks book. In the DT database is a Notes group that indexes the book/ folder. With the “hide system files” setting of Notebooks turned on that works perfectly. The arrangement is bi-directional; if I edit a note in DT or create a new one the changes are seen in Notebook. I can even “open with…” in DT and use my default markdown editor (Typora).
The icing on the cake is that I have a separate book in Notebooks (unimaginatively called Inbox) that is shared with Unclutter notes. I can quickly jot reminders to myself and transient/ ephemeral stuff in Unclutter to process later in Notebook. All that took was replacing Unclutter’s note folder with a soft link to Notebooks’ folder.