If that is the case then opening the instances is not the way you want to do it. How you do things via the UI can often be very different from via a script.
For instance, if you want to copy an instance you click on into the root context then you can create a Ruby tool and use the pick helper to pick instances in the model. The pick helper will also give you the transformation for the pick. Using that you can add a new instance entities.add_instance using a transformation which will place it in a visual identical position as the one you picked.
(This is a good example of including your desired result when asking programming questions - as the solution to your end result might be different that the path you’re looking at.)