@lukearh
Its a workflow you can find lots of online resources on this topic. Simply underlaying or linking a model regardless if it is IFC/RVT/DWG or whatever format is not really collaboration 🙂 ... at least in MPO. And usually when an architect and a structural engineer collaborate, they have shared key elements between their models.
Some collaborate based on that principle with the goal to achieve a confederated model at the end and others prefer to live in the world of their own discipline and simply stick to underlays (unconventional collaboration) this is where you resort to graphic tricks to achieve the clean up you are after. Example: Below Gif is a Model with IFC Structural columns masking the walls in an Architectural Model...
Sorry I cannot elaborate more on the topic during office hours
