EnergyPlus doesn’t model air temperature differences within individual Rooms/Zones and so neither do the thermal maps. Granted, EnergyPlus does a relatively decent job accounting for heat transfer that results from stratification (for example, using less resistive thermal coefficients for RoofCeilings than for Floors) and the EnergyPlus AFN can model buoyancy driven flow from room to room (as long as the flow is uni-directional as you might find between an atrium and its adjacent rooms). The thermal maps will also interpolate air temperature values across air boundaries so that you don’t get a harsh transition of air temperatures across a boundary that doesn’t actually exist.
I think I answered your question about the recommended say of doing this here: