Just wanted to finish this off this thread with some good news.
The solution that works for me is:
- Build the app in Xcode
- Sign the entire app with SD Notary
- Build the DMG with DropDMG
- Notarize the DMG with terminal
I realise step 4 could be done with SD Notary and maybe even step 3 too with the new feature to link to DropDMG, but for now this is working consistently well and I can get on with everything else
Thanks again for you help. Much appreciated.