I've replied to the thread explaining why this is expected behavior https://forum.unity.com/threads/runtime-scene-serialization-package-status.1168783/#post-8269929
The warnings are there to tell the user that the system does not have enough information to serialize the scene at runtime. The issue is that they have a prefab in the scene which will be saved as a prefab reference to the AssetPack, but then they try to save that scene in Play mode, where the prefab is unpacked and the system does not have references to the assets it references.