The RuntimeInitializeLoadType.BeforeSceneLoad callbacks are invoked very early in the load scene operation of the first scene: just after the objects are loaded in memory but before Awake and OnEnable is called. So basically you get this callback before the objects loaded have been fully setup. The change in behavior for finding active objects is here to stay since objects are not actually 'activated' before Awake and OnEnable are called. This change was need to fix various systems.
What you need to do now when using callbacks that are invoked before Awake() is to get all inactive objects and use the state for 'activeSelf' and manually check if the object will be active after Awake() by checking all parents are also activeSelf. In other words activeInHierarchy will always return false until the GameObjects have been awakened.
The docs for RuntimeInitializeLoadType are incorrect and will be corrected to match when these callbacks are invoked and more info about the lifetime object state.

Example:

class MyClass
{
[RuntimeInitializeOnLoadMethod(RuntimeInitializeLoadType.BeforeSceneLoad)]
private static void FirstSceneLoading()
{
var components = UnityEngine.Object.FindObjectsByType(typeof(MonoBehaviour), FindObjectsInactive.Include, FindObjectsSortMode.None);
var willBeActiveAfterSceneLoad = 0;
foreach (var c in components)
{
if (WillBeActiveAfterSceneLoad(((Component)c).gameObject))
willBeActiveAfterSceneLoad++;
}
Debug.Log("BeforeSceneLoad. Will be Active after Awake, count: " + willBeActiveAfterSceneLoad);
}

static bool WillBeActiveAfterSceneLoad(GameObject gameObject)
{
Transform current = gameObject.transform;
while (current != null)
{
if (!current.gameObject.activeSelf)
return false;

current = current.parent;
}

return true;
}
}

The RuntimeInitializeLoadType.BeforeSceneLoad callbacks are invoked very early in the load scene operation of the first scene: just after the objects are loaded in memory but before Awake and OnEnable is called. So basically you get this callback before the objects loaded have been fully setup. The change in behavior for finding active objects is here to stay since objects are not actually 'activated' before Awake and OnEnable are called. This change was need to fix various systems.
What you need to do now when using callbacks that are invoked before Awake() is to get all inactive objects and use the state for 'activeSelf' and manually check if the object will be active after Awake() by checking all parents are also activeSelf. In other words activeInHierarchy will always return false until the GameObjects have been awakened.
The docs for RuntimeInitializeLoadType are incorrect and will be corrected to match when these callbacks are invoked and more info about the lifetime object state.

Example:

class MyClass
{
[RuntimeInitializeOnLoadMethod(RuntimeInitializeLoadType.BeforeSceneLoad)]
private static void FirstSceneLoading()
{
var components = UnityEngine.Object.FindObjectsByType(typeof(MonoBehaviour), FindObjectsInactive.Include, FindObjectsSortMode.None);
var willBeActiveAfterSceneLoad = 0;
foreach (var c in components)
{
if (WillBeActiveAfterSceneLoad(((Component)c).gameObject))
willBeActiveAfterSceneLoad++;
}
Debug.Log("BeforeSceneLoad. Will be Active after Awake, count: " + willBeActiveAfterSceneLoad);
}

static bool WillBeActiveAfterSceneLoad(GameObject gameObject)
{
Transform current = gameObject.transform;
while (current != null)
{
if (!current.gameObject.activeSelf)
return false;

current = current.parent;
}

return true;
}
}