I think if we could use the AirflowNetwork:MultiZone:Component:HorizontalOpening for an AirBoundary Surface, we would have a pretty robust way of doing this in EnergyPlus. The biggest limitation of the current setup is that airflow can only be uni-directional across an AirBounday. But from conversations with the E+ developers, I think they are open to allowing us to use the HorizontalOpening object for AirBoundaries if enough people ask for it. This would allow us to model the bi-directional airflow that you would expect across horizontal AirBoundaries of a stratified atrium.
So this might be a good thing to mention on UnmetHours.