Unfinished Spaces Baseline and Proposed System

Hello: I have a 3 story mixed use healthcare facility with offices, exam rooms, treatment rooms, research areas, and a surgical suite. Each floor has some unfinished shelled spaces (total is less than 40%). I understand that the unfinished spaces need to be held neutral and modeled the same in the baseline and proposed. My baseline system is System 5 with a rooftop unit per floor. My proposed HVAC system is chilled water and hot water VAV AHUs. The shelled spaces have ducts and hot water piping capped in the shelled space for future connection when the spaces are built out. My question relates to how to model the proposed and baseline shelled spaces. For the proposed I was going to model them as a finished design with each shelled space on its respective AHU. For the baseline I was going to model the shelled spaces as one packaged AHU with VAV reheat per zone with the same parameters as the proposed (flow minimums, setpoints, etc.). Would this be an appropriate way to model the unfinished spaces? Or should I model the proposed the same as the baseline (packaged AHU with VAV reheat with all parameters as indicated in Appendix G)? Any input is appreciated.