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If you pick the same building type, the same template, and only change the climate zone, here's what will change:

• The weather, water mains, and ground temperatures
• The construction (envelope) properties
• The autosized capacities of the HVAC equipment, which may lead to
  • Different HVAC equipment efficiency levels
  • Different HVAC system controls

So while the type of HVAC system is the same, some of the details of how it performs and how it is controlled can be different.

These documents (listed oldest to most current) describe the models in detail:

• U.S. Department of Energy Commercial Reference Building Models of the National Building Stock
• Achieving the 30% Goal: Energy and Cost Savings Analysis of ASHRAE Standard 90.1-2010
• Enhancements to ASHRAE Standard 90.1 Prototype Building Models