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Don't add any HVAC system serving the zone.

See the DetermineBuildingFloorArea in OutputReportTabular.cc:

if ( Zone( iZone ).isPartOfTotalArea ) {
        buildingGrossFloorArea += curZoneArea;
        // If a ZoneHVAC:EquipmentConnections is used for a zone then
        // it is considered conditioned. Also ZONE SUPPLY PLENUM and ZONE RETURN PLENUM are
        // also is considered conditioned.
        if ( Zone( iZone ).SystemZoneNodeNumber > 0 ) {
            buildingConditionedFloorArea += curZoneArea;
        }
    }

Don't add any HVAC system serving a thermostat to the zone.zone that are unconditioned?

See the DetermineBuildingFloorArea in OutputReportTabular.cc:

if ( Zone( iZone ).isPartOfTotalArea ) {
        buildingGrossFloorArea += curZoneArea;
        // If a ZoneHVAC:EquipmentConnections is used for a zone then
        // it is considered conditioned. Also ZONE SUPPLY PLENUM and ZONE RETURN PLENUM are
        // also is considered conditioned.
        if ( Zone( iZone ).SystemZoneNodeNumber > 0 ) {
            buildingConditionedFloorArea += curZoneArea;
        }
    }