Unity Editor utility class to hack a native overlay window into the scene view.

SceneOverlayWindow.cs

using System;
using System.Reflection;
using UnityEditor;
using UnityEngine;

public class SceneOverlayWindow
{
    private object sceneOverlayWindow;
    private MethodInfo showWindow;
    public UnityEngine.Object target;

    // public delegate void ShowWindowFunc(object overlayWindow);
    public delegate void OnWindowGUICallback(UnityEngine.Object target, SceneView sceneView);

    public SceneOverlayWindow(GUIContent title, OnWindowGUICallback onWindowGUI, UnityEngine.Object target, int priority = int.MaxValue)
    {
        this.target = target;
        var unityEditor = Assembly.GetAssembly(typeof(UnityEditor.SceneView));
        var overlayWindowType = unityEditor.GetType("UnityEditor.OverlayWindow");
        var sceneViewOverlayType = unityEditor.GetType("UnityEditor.SceneViewOverlay");
        var windowFuncType = sceneViewOverlayType.GetNestedType("WindowFunction");
        var windowFunc = Delegate.CreateDelegate(windowFuncType, onWindowGUI.Target, onWindowGUI.Method);
        var windowDisplayOptionType = sceneViewOverlayType.GetNestedType("WindowDisplayOption");
        sceneOverlayWindow = Activator.CreateInstance(overlayWindowType, 
            title,
            windowFunc,
            int.MaxValue, this.target, 
            Enum.Parse(windowDisplayOptionType, "OneWindowPerTarget") //SceneViewOverlay.WindowDisplayOption.OneWindowPerTarget
        );
        showWindow = sceneViewOverlayType.GetMethod("ShowWindow", BindingFlags.Static | BindingFlags.Public);

        // showWindow = Delegate.CreateDelegate(typeof(ShowWindowFunc), showSceneViewOverlay) as ShowWindowFunc;
    }

    public void ShowWindow()
    {
        this.showWindow.Invoke(null, new object[]{sceneOverlayWindow});
    }

}