Unity editor script for better editing of prefabs. Put in Assets/Editor.

EditPrefabInScene.cs

using UnityEngine;
using UnityEditor;
using UnityEditor.SceneManagement;
using UnityEngine.SceneManagement;

// From https://gist.github.com/JohannesDeml/5802473b569718c9c86de906b7039aec
// Original https://gist.github.com/ulrikdamm/338392c3b0900de225ec6dd10864cab4
// Adds a "Edit Prefab" option in the Assets menu (or right clicking an asset in the project browser).
// This opens an empty scene with your prefab where you can edit it.
// Put this script in your project as Assets/Editor/EditPrefab.cs


public class EditPrefabInScene
{
	private static Object GetPrefab(Object selection)
	{
		if (selection == null)
		{
			return null;
		}
		var prefabType = PrefabUtility.GetPrefabType(selection);
		if (prefabType == PrefabType.PrefabInstance)
		{
			var prefab = PrefabUtility.GetPrefabParent(selection);
			return prefab;
		}

		if (prefabType == PrefabType.Prefab)
		{
			return selection;
		}

		return null;
	}

	[MenuItem("Assets/Edit prefab")]
	public static void EditPrefab()
	{
		var prefab = GetPrefab(Selection.activeObject);

		EditorSceneManager.SaveOpenScenes();
		var currentScenes = new SceneSetupWrapper();
		currentScenes.TakeSnapshot();

		var scene = EditorSceneManager.NewScene(NewSceneSetup.DefaultGameObjects, NewSceneMode.Single);
		var instance = (GameObject) PrefabUtility.InstantiatePrefab(prefab, scene);
		Selection.activeObject = instance;
		SceneView.lastActiveSceneView.FrameSelected();

		var returnHandler = new ReturnToSceneGUI();
		returnHandler.PreviousSceneSetup = currentScenes;
		returnHandler.PrefabInstance = instance;
	}

	[MenuItem("Assets/Edit prefab", true)]
	public static bool EditPrefabValidator()
	{
		var prefab = GetPrefab(Selection.activeObject);
		return prefab != null;
	}
}

public sealed class SceneSetupWrapper
{
	private string[] scenePaths;
	private bool[] scenesLoaded;
	private int activeSceneIndex;

	public void TakeSnapshot()
	{
		int sceneCount = SceneManager.sceneCount;
		scenePaths = new string[sceneCount];
		scenesLoaded = new bool[sceneCount];
		var activeScene = SceneManager.GetActiveScene();
		for (int i = 0; i < sceneCount; i++)
		{
			var scene = SceneManager.GetSceneAt(i);
			scenePaths[i] = scene.path;
			scenesLoaded[i] = scene.isLoaded;
			if (scene == activeScene)
			{
				activeSceneIndex = i;
			}
		}
	}

	public void OpenSetup()
	{
		if (scenePaths.Length == 0)
		{
			Debug.LogError("Can't open scene setup, no data stored.");
			return;
		}
		try
		{
			bool canceled = false;
			int sceneCount = scenePaths.Length;
			canceled = EditorUtility.DisplayCancelableProgressBar("Loading scenes",
					"Loading scenes from Setup", (float)0 / sceneCount);

			Scene activeScene = EditorSceneManager.OpenScene(scenePaths[0]);

			if (canceled)
			{
				EditorUtility.ClearProgressBar();
				return;
			}
			for (int i = 1; i < sceneCount; i++)
			{
				canceled = EditorUtility.DisplayCancelableProgressBar("Loading scenes",
					"Loading scenes from Setup", (float)i / sceneCount);
				if (canceled)
				{
					EditorUtility.ClearProgressBar();
					return;
				}
				var openSceneMode = scenesLoaded[i] ? OpenSceneMode.Additive : OpenSceneMode.AdditiveWithoutLoading;
				var scene = EditorSceneManager.OpenScene(scenePaths[i], openSceneMode);
				if (activeSceneIndex == i)
				{
					activeScene = scene;
				}
			}
			SceneManager.SetActiveScene(activeScene);
		}
		finally
		{
			EditorUtility.ClearProgressBar();
		}
	}
}

public sealed class ReturnToSceneGUI
{
	public SceneSetupWrapper PreviousSceneSetup;
	public GameObject PrefabInstance;
	private GUIStyle style;

	public ReturnToSceneGUI()
	{
		SceneView.onSceneGUIDelegate += RenderSceneGUI;
		style = new GUIStyle();
		style.margin = new RectOffset(10, 10, 10, 10);
	}

	public void RenderSceneGUI(SceneView sceneview)
	{
		Handles.BeginGUI();
		GUILayout.BeginArea(new Rect(20, 20, 180, 300), style);
		var rect = EditorGUILayout.BeginVertical();
		GUI.Box(rect, GUIContent.none);

		if (GUILayout.Button("Apply and return", new GUILayoutOption[0]))
		{
			PrefabUtility.ReplacePrefab(PrefabInstance, PrefabUtility.GetPrefabParent(PrefabInstance), ReplacePrefabOptions.ConnectToPrefab);
			SceneView.onSceneGUIDelegate -= RenderSceneGUI;
			PreviousSceneSetup.OpenSetup();
		}

		if (GUILayout.Button("Discard changes", new GUILayoutOption[0]))
		{
			SceneView.onSceneGUIDelegate -= RenderSceneGUI;
			PreviousSceneSetup.OpenSetup();
		}

		EditorGUILayout.EndVertical();
		GUILayout.EndArea();
		Handles.EndGUI();
	}
}

It seems that DisplayCancelableProgressBar is known to cause these NullReferenceExceptions, although it doesn't seem to do any harm.
I resolved it by adding
EditorGUIUtility.ExitGUI();
After each of the
EditorUtility.ClearProgressBar();

Not very important, but some of your solution is depreciated:
onSceneGUIDelegate
is replaced with
duringSceneGui

The prefabType is replaced with prefabAssetType, and ReplacePrefab -> SaveAsPrefabAssetAndConnect