Serializing object in scene?

For my physics engine, I'm trying to have objects be able to be created in the scene and left in there for run-time. The starting position is stored in integers and they have to be serialized before run-time for determinism.

So far, I've managed to serialize the variables with EditorUtility.SetDirty:

 public override void OnInspectorGUI ()
 {
     target.StartX = (long)transform.position.x;
     etc.
 
     EditorUtility.SetDirty (target);
 }

Unfortunately, this serializes the variables for all prefabs and clones of the object, even ones that are in the scene before run-time as well. Is there a way to serialize variables individually for objects like how positions are serialized?