Major cleanup of the prefab generator.  Turns out if a game object is disabled, all its children will act as if they are disabled.  If one of those children is say, Instantiated and reparented - it becomes active automatically.  A "deactivator" game object was added to be the parent of the prefab resources, which is disabled and flagged as DontDestroy.  This eliminated the need for a post PSystem spawn stage making prefab rewriting the only required step.