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Could you not model the top of the plenum and the bottom of the next floor with a 1' gap, meaning they are not directly adjacent when you look at the vertexes. This would be similar to modeling a building floor when using a multiplier.

This would respect the volumes of both spaces as well as elevation. It would probably not solve exterior wall area.

Another potential issue with this approach in OpenStudio is the surface matching algorithm. It would not recognize those offset surfaces as 'adjacent' when you intend for them to be adjacent. One possible (untested) workaround is to have all the surfaces truly adjacent, run surface matching algorithm, then offset all surfaces.