As the original author of the Reference Buildings back in 2005-2007, I can say that the selection of HVAC types and zoning are based partly, maybe largely, on "engineering judgement", and partly on CBECS to confirm or substantiate the said "engineering judgement". Furthermore, there's a history behind the Reference Buildings dating back to work done for the Gas Research Institute in the early 90s, during which I went over with an engineer (the late Bruce Birdsall) the various building types and decided the most prevalent HVAC systems then being used. When DOE asked me to update the GRI work for the Reference Building, I analyzed the latest CBECS and apparently so did Dave Winiarski at PNNL and made changes where appropriate. I found some issues such as: (1) the prevalence of HVAC system or fuel mix may differ in different parts of the country, (2) for some building types and/or climates there were several (esp. two) HVAC systems or fuel mix of similar prevalence. Since I haven't been involved in this work since 2007, I don't know how these issues since have been resolved or treated. My main suggestion on interpreting the HVAC system configurations and zoning in these Reference Buildings is to regard them as the best shot effort by whoever was doing it to characterize with a single model a diverse building/HVAC population, and take it from there.

As a more general explanation, when you're designing HVAC systems that serves multiple zones, you want to make sure that all the zones being served have similar loads and schedules. Otherwise, you end up running the entire system just because of one zone, which wastes energy. Because you sometimes have zones that are outliers, instead of putting them on the multi-zone system, you give them their own system. Another reason to put a particular zone on a separate system is if that zone is physically far away, and it wouldn't make sense to run ductwork/piping that distance.

Here's what this logic looks like when applied to the Secondary School Reference Building:

• Each wing has a VAV system serving the classrooms, offices, and corridors on the wing.
• Each of the very different zones (gym, auditorium, kitchen, etc.) gets its own packaged single zone unit.

You can see this logic described pretty concisely in ASHRAE 90.1-2010 Appendix G:

G3.1.1 Baseline HVAC System Type and Description

"...If the baseline type is (a multizone system type), use separate single-zone systems...for any spaces that have occupancy or process loads or schedules that differ significantly from the rest of the building. Peak thermal loads that differ by 10 Btu/hr*ft2 or more than 40 full load hours per week are considered to differ significantly..."

The Technical Report (pdf link) for the Commercial Reference Building Models should have most of the answers to your questions.

The Review of Pre- and Post-1980 Buildings in CBECS – HVAC Equipment has details about the specific reasons that certain HVAC systems are used for certain building types, as well as why the hotel, for example, uses two different systems (on page 19). It appears that the modelers based their decisions on the statistical likelihood of a type of HVAC system being implemented in a certain living space, and only put multiple types of systems in a building if the data showed a clear divide.