UFAD System: Underfloor plenum in baseline model?

The proposed design is an Underfloor Air Distribution (UFAD) system utilizing an underfloor supply plenum and overhead return plenum. I am setting up the baseline model for LEED submission. The proposed building stories and area put us into Baseline HVAC System Type 5 (Packaged VAV w/ Reheat). My question is whether or not to include the underfloor plenum in the baseline model to be consistent with the envelope areas exposed to the space in the proposed building, even though the baseline will use an overhead delivery system. We are referencing ASHRAE 90.1-2007. Table G3.1 notes that the total gross area of exterior walls shall be the same in proposed and baseline, but does not mention whether the same envelope area must be distributed equally to plenums vs. spaces between the proposed and baseline. We are modeling with Trane TRACE 700. I am able to create the underfloor plenum in the baseline rooms, but when the overhead baseline system type 5 is applied, I am unable to enter underfloor plenum heights and raised floor heat transfer coefficients on the systems tab. TRACE help says that if a room has an underfloor plenum but is not assigned to a system with a UFAD supply, the plenum will be modeled as dead air space. Then how does TRACE model heat transfer between the dead air space and the room if I was unable to tell it a heat transfer coefficient of the raised floor assembly? I have the software's tech support looking into this as well. But my guess is someone has modeled proposed UFAD vs. baseline overhead VAV before using TRACE, and I'm wondering how they might have handled it. Thanks for the help.