Question-and-Answer Resource for the Building Energy Modeling Community
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You should follow ASHRAE 90.1 G.3.1.1, but in my understanding, this is a minimum requirement (i.e. VAV systems on two or more floors should not be combined), and the VAV system on one floor should be further separated according to other requirements.
For example, if some zones in the proposed case have MERV13 Filter and other zones does not have it, the VAV systems in the Baseline case should be separated because the Fan Power Limitation Pressure Drop Adjustment is different as per Table 6.5.3.1-2.
If some zones in the Proposed case include humidification and other zones does not include it, the VAV systems in the Baseline case should be separated into those with humidification and those wihtout humidification as per Table G3.1 10.HVAC Systems.
Please also refer to other requirements in Appendix G.
By the way, I think you don't need to worry about whether the Baseline case is realistic or not. There are many requirements in the Baseline case that are not realistic, such as fixed pump head, no matter how large the building is.
