I think you have to enable “Allow downgrade” for the AU bundle in your Packages project, see link below for the screenshot where to find it.
Beware that when you remove a bundle from the Packages project and then re-add it, the “Allow downgrade” checkbox for it resets to unticked, so you have to remember to re-enable it whenever you add a new bundle/binary to the project.
I have scripted that with a good deal of python that parses the Packages project, it’s a .plist file after all