Apologies for dragging this up again, cleanly shutting down deluge seems to have been a problem since it's inception lol. I have managed to 'Quit & Shutdown Daemon' from the windows client as mentioned above (does option not exist in the web client?), which seems to have resolved most of the issues I had previously with stopping the docker container from unraid.
The issue I'm having now is that the daemon restarts itself. So if I need to shutdown the container for whatever reason I have to 'Quit & Shutdown Daemon', wait long enough that it shuts down cleanly, but not too long or it will have started again.
I assume there's something in the Binhex container that's recognizing that the process is no longer running and starting it up again? Can I stop this somehow?