I don't know if Unity staff will see this, but I believe I spotted a bug in the Unity.Scenes system.
Inside ResolveSceneReferenceSystem's OnCreate, there is a GetExistingSystem<SceneSystem>(). I believe it should be GetOrCreateSystem<SceneSystem>(). Otherwise, if systems are created in the wrong order, ResolveSceneReferenceSystem gets a null entity.
That's the issue I encountered when I made my own world bootsrap.