Floor area reduced when adding vertically stacked spaces into a single thermal zone

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When I put two vertically stacked spaces into one thermal zone in OpenStudio. The simulation results shows that the floor area is just half of the total floor area. Even though I have checked the "Part of Total Floor Area" in OpenStudio for each space. Looks like the internal gains (people, lights, electric equipments) were defined as per floor area, so I assume in EnergyPlus simulation they are also reduced by half. Is that what's expected?