Baseline HVAC System for Floors with Conditioned Spaces with no Ventilation

Separate system 3 or 4 should be used when the occupancy, process load, or schedule are significantly different. Section G3.1.1 doesn't list a scenario where ventilation will exclusively determine the baseline system type.  As for how to model ventilation in the baseline, I've used judgement in the past. When it's not critical, I'd just model it to be a percentage of total supply CFM on the system level. If it is critical, I'll model it on the zone level (which is more work!). That way, your baseline will account for the entire OA CFM and floor system will auto-size. I suggest you start by setting the zone OA for those zones not receiving ventilation to zero, and auto-size the rest, and see how it goes.