I’m looking for a way I can mark objects instantiated by my editor script in a way that my script can recognize when checking the scene but the user will never see.
That depends on what your object are doing. If it just are going to hold a bunch of scripts, you should create an “Empty GameObject”. It is a mesh (object) that you want to see in the editor, you should set the object to be inactive in your script, like this:
yourObject.SetActive( false );
By doing that, I think you will be able to acces the object, because you have reference to it before you set it to be inactive. Correct me if I’m wrong.