I was able to get in contact with Apple engineers during a WWDC21 - Sign in with Apple dedicated lab and they explained me how to solve this. Adding multiple apps to the same App ID is meant for apps of the same target but running on a different platform (e.g. iOS app, macOS app, watchOS app, etc.). The solution is to enable each app as primary ID for Sign in with Apple. When triggering the Sign in with Apple request from within the app, this returns a JWT token which will be used for proceeding with the authentication creation/identification in your backend. This token contains a unique user id, found under the sub key, which is created from the combination of your team/developer account ID and the user's Apple ID; This value is then unique in your developer account and it means that the combination of the user Apple ID and your team ID associated with your app(s), will always generate the same value for the sub field. This will identify the user across the apps so that your backend can avoid generating a new account but instead return the existing, associated one.

I just stumbled upon the same problem. I have several apps (~20) which need to be able to log in with the same account across apps. Internally, we create some sort of organization account, so that users can login seamlessly in every app and have the content synced. How can be this achieved via Sign in with Apple? If the maximum number of apps to be grouped together is 5, what should I do with the other ~15 then?!

Any updates on this?

I have the same problem but with com.apple.developer.icloud-container-identifiers key. Moreover, the build I uploaded never reached App Store Connect after ~40 minutes