Programmatically apply additions to prefabs hierarchy after addition via editor script

Unity Engine
1

I’m having a hard time unraveling Unity’s complexity with prefabs management and the PrefabUtility.
I made an editor script that adds a few components to the active scene.
I process all game objects that were affected by doing (simplifying a bit)

if (PrefabUtility.IsPartOfAnyPrefab(go))
{
    GameObject prefabContainer = PrefabUtility.GetOutermostPrefabInstanceRoot(go);
    EditorUtility.SetDirty(prefabContainer);
    PrefabUtility.ApplyPrefabInstance(prefabContainer, InteractionMode.AutomatedAction);
}

I would have thought this was enough but it is not applying correctly to the prefabs I want (they always remain as overrides) and considering some scenes have nested prefabs, prefab variants, prefab variants nested into prefabs, and so on, I kind of figured this would happen so what I really need to know is
How do I collect all the prefabs (variants, roots, prefab containers of prefab containers…) that need an “apply” after adding a component to a game object that’s in their (descendant) hierarchy?
Thanks all!

2

Maybe you are missing some GameObject in your list. How do you get the list of all GameObjects currently in scene? And yet, consider that you might have some Prefab that is not instantiated in your scene.