To be clear Someone needs to insert the subtraction into the model.
The MEP modeler will usually be responsible for proposing the size of the opening. These days he will need to know how much to oversize the opening, chase or pocket for the outlet, drainage channel or duct etc.
He will need to come up with minimum size to avoid weakening the structure too much but allows for enough room for the epoxy mortar, fire stopping, damper etc to work, given the tolerances of the substrate at hand.
He will also need to coordinate with structural engineer with regards to the spacing and sizes of the openings as substrates like holorib will have restrictions especially if fire compartmentation is required. The structural engineer will want to minimise the amount of trimmers he will need to provide.
In masonry walls, he will also need to look at whether lintels are required and size them accordingly. He may also need to move the windposts and MJs around to accommodate the penetration.
There will also be other considerations like acoustics, and inspectability and replacement of things like all that fire mastic and intumescent paint.
Then it goes to the structural engineer usually has to accept the results and modify his structure to suit. Only if it is absolutely impossible will there be a redesign of the MEP system which will be very expensive.
Trust me, you want to have the option to have auto subtractions. The rule is usually, the structural engineer doesn't even show any openings less than 100-200-300mm. Keeps getting bigger over the years.
What is needed is a means of tracking the changes when the structural engineer receives the shared model. Revit has its copy monitor tool. I suppose we have design history.
The subtractions need to parametric and linked to the duct etc. You don't want a modeler doing this manually. Overrides are inevitable but the bulk of it should be parametric.