BTW, I figured out the lock file issue waking from a dream in the middle of the night, but your second response would have led me to it without that sudden enlightenment.

Resolved. You are correct. Any additional content apart from the app will make Xcode treat it as content. I followed through and the directory contained a lock file used as a workaround for the inability to have a custom script for the Clean Product option. Since we use Qt integrated into the project, cleaning requires some extra directories to be cleaned up. I moved that function to a prebuild script that was triggered by the absence of a lock file in the project. Removing it and just testing for the App Bundle shell resolved the issue. We can now use Developer ID/Notarization or App Store submission from the Organizer. Thanks for your help.

BTW, the Distribute App vs Content is a very good lead I will investigate further.

Thank you, The exported archive has the full app that you can run. It is not a dependent target. Exporting the archive I can double-click on the app, it is complete and runs fine. This used to work, what could have changed? How can I tell Xcode to treat this as an app?

I have looked at trying different signing options. I am using Automatic and tested Apple Developer, Developer, and Developer ID - Application, which we use in command line signing and notarization.