Updated code to get a Unity object id.

ObjectTools.cs

#define UNITY_5_PLUS
#if UNITY_4_5 || UNITY_4_6 || UNITY_4_7 || UNITY_4_8 || UNITY_4_9
#undef UNITY_5_PLUS
#endif

using UnityEngine;
using System.Reflection;
using UnityEditor;

namespace CodeStage.Maintainer.Tools
{
	public class ObjectTools
	{
		private static PropertyInfo cachedInspectorModeInfo;

		internal static long GetLocalIdentifierInFileForObject(Object unityObject)
		{
			long id = -1;

			if (unityObject == null) return id;

			if (cachedInspectorModeInfo == null)
			{
				cachedInspectorModeInfo = typeof(SerializedObject).GetProperty("inspectorMode", BindingFlags.NonPublic | BindingFlags.Instance);
			}

			SerializedObject serializedObject = new SerializedObject(unityObject);
			cachedInspectorModeInfo.SetValue(serializedObject, InspectorMode.Debug, null);
			SerializedProperty serializedProperty = serializedObject.FindProperty("m_LocalIdentfierInFile");
#if UNITY_5_PLUS
			id = serializedProperty.longValue;
#else
			id = serializedProperty.intValue;
#endif
			if (id <= 0)
			{
				PrefabType prefabType = PrefabUtility.GetPrefabType(unityObject);
				if (prefabType != PrefabType.None)
				{
					id = GetLocalIdentifierInFileForObject(PrefabUtility.GetPrefabParent(unityObject));
				}
				else
				{
					// this will work for the new objects in scene which weren't saved yet
					id = unityObject.GetInstanceID();
				}
			}

			if (id <= 0)
			{
				GameObject go = unityObject as GameObject;
				if (go != null)
				{
					id = go.transform.GetSiblingIndex();
				}
			}

			return id;
		}
	}
}

there is a more elegant way

You are wrong. This wont work for Components that is inside the scene. For that reason, they created some kind of ID Obtainer named "GlobalObjectId". It works if you want to get the ID and GUID. But still, if you want to check if it is an instantiation or persistent, when you check a new instantiation via GlobalObjectID, hilarously it creates a new whole localID and assigns the GUID. So currently, they just blocked all of the ways to check whether it is instantiated or not. From the first stage, they should have been added that into their UnityEngine.Object hence it is not System.Object .D