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If large areas (over 20,000 SF) meet this definition the corresponding thermal zones can be grouped together into a separate system type per exception a:

"Use additional system type(s) for nonpredominant conditions (i.e., residential/nonresidential or heating source) if those conditions apply to more than 20,000 ft2 of conditioned floor area."

Exception a. should dramatically reduce the total amount of zones that require system type 3 or 4.

We regularly perform energy modeling for laboratory buildings (and design them) and commonly all of the laboratory spaces are on a single system type (as they often have specific ventilation requirement and schedule requirements) separate from the non-lab spaces such as offices/conference rooms, etc. You may have a two systems of type 5/6/7/8s on a single floor along with several system types 3 or 4 for small rooms that have additional specialty loads or schedule requirements (a cold environment room as an example).

I have not dived into how the building rotations impacts this exercise as I interpret the requirement only to apply to the base rotation. A dedicated system could be provided to a particular facade spanning multiple floors per exception a. if the zones on that facade were dramatically different than the predominant space type in the rest of the building.