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After reading through the EnergyPlus Engineering Reference 9.2.0, I found this:
While the unitary system may be configured to serve multiple zones, system operation is controlled by a thermostat located in a single “control” zone. ... If EnergyPlus determines that the unitary system must supply heating to the control zone to meet the zone air temperature setpoint, then the unitary system model computes the total sensible heating load to be delivered to the zones being served based on the control zone sensible heating load and the control zone airflow fraction.
UnitarySystemHeatingLoad = ControlZoneHeatingLoad / ControlZoneAirFlowFraction (16.275)
What I understood from this is that the thermostat setpoints are still significant even-though you are manually setting the sensible heating/cooling load. I changed the thermostat setpoint for the controlled zone via EMS and the heating energy delivered by the system reflected the input heating setpoint.
Hope this helps folks with similar issues. Also, if someone can confirm this that would be great.
Thanks.