Problem with loading scene asynchronously and creating objects on Awake

I created a system with a scene loader, which loads scenes asynchronously, then unloads the previous scene. The scene loader "lives" in its own scene "SceneLoader", but gets marked as "DontDestroyOnLoad", so it is removed from the actual scene hierarchy. So when I start the game with the scene loader scene as a start scene, in the hierarchy I have the "SceneLoader", which has no objects, and the "DontDestroyOnLoad" section, which houses the GameObjects of my scene loader.
In the scenes I am loading, there are several scripts, that create GameObjects in the Awake function. When this happens, they do not get placed into the newly loaded scene, but into my "SceneLoader" scene. It seems like Awake is called before the new scene is completely initialized. I am currently using a workaround and move the misplaced objects back to the scene where they belong, but this seems like a hack and not intended behaviour.
I am using Unity 5.4. Is this a known bug in this version or is this intended behaviour? Am I doing something wrong?

 

This thread may help you:

https://forum.unity3d.com/threads/scenemanager-loadscene-additive-and-set-active.380826/

The bottom line is that the scene in bold is the "active" scene and all instantiated objects will go under it. You have to change the active scene via SceneManager.SetActiveScene if you want instantiated objects to go somewhere else.

 

Ok, so if I understand that correctly, there is no way, to switch the active scene *before* Awake() is called on the objects of the new scene, since it is technically not loaded and can not be set to active before? So I can only help myself with the workaround of moving the objects, and then set the scene to active after that, correct?