Using GetOutermostPrefabInstanceRoot on a component that is not an instance will return null. When opening Prefab Mode the Prefab asset contents is loaded from the .prefab source file and the components here are no longer from an instance'. In Prefab Mode you here are allowed to make structural changes unlike prefab instances in the scene where restructuring is prohibited. So this is an important distinction: when opening Prefab it is no longer the instance with its potential overrides you are seeing but the actual prefab asset objects.

In order for your script to support Prefab Mode I have modified the start of your script as follows:

private static IEnumerable<NestedPrefabInfo> FindNestedPrefabReferencesTo(UnityEngine.Component obj)
{
string prefabPath = string.Empty;
GameObject prefabRoot = PrefabUtility.GetOutermostPrefabInstanceRoot(obj);
if (prefabRoot != null)
{
// Handle prefab instances in the scene
prefabPath = PrefabUtility.GetPrefabAssetPathOfNearestInstanceRoot(prefabRoot);
}
else
{
// Handle Prefab Mode
var prefabStage = PrefabStageUtility.GetPrefabStage(obj.gameObject);
if (prefabStage != null)
{
prefabRoot = prefabStage.prefabContentsRoot;
prefabPath = prefabStage.prefabAssetPath;
}
}

if (prefabRoot != null)
{
List<HierarchyInfo> hierarchy = GetHierarchyStructure(obj.transform, prefabRoot.transform);

// iterate all prefabs in project
foreach (GameObject prefab in IterateAllPrefabs())
...