Enabling a library override shouldn't reset transform

I would like a way to keep the modified transform of a linked collection when I do a library override. Scenario: Master blend with product files. Another blend file for shots. It has many scenes with the product collections linked into it (from Master.blend) and instanced into each scene. All is well until one of the shots needs a material change on the product. The collection has been moved into place, the camera is setup, the lighting is right... library override to change a material and boom, the transform of the entire collection is reset.

I'd like the option to keep the modified transform data. I must be using linked collections wrong as I can't understand how anyone could make use of linked collections and library overrides without this feature.