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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.

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, I separate HVAC systems for zones with DCV and for zones wihtout DCV on the same floor. DCV will not work properly 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.these zones are served by single HVAC system.

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.

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.

I separate HVAC systems for zones with DCV and for zones wihtout without DCV on the same floor. DCV will not work properly if these zones are served by single HVAC system.

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 without 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.

Addendum

According to the 90.1 User's Manual, if a floor has zones with various cooling thermostat setpoints, they does not need to be separated. One system should serve them. The supply air temperature should be 11C below the lowest cooling thermostat setpoint.

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.

I separate HVAC systems for zones with DCV and for zones without DCV on the same floor. DCV will not work properly if these zones are served by single HVAC system.

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 without 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.

Addendum

According to the 90.1 User's Manual, if a floor has zones with various cooling thermostat setpoints, they does do not need to be separated. One system should serve them. The supply air temperature should be 11C below the lowest cooling thermostat setpoint.