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To answer your question - I had some projects in the past that had several zones (over 100+) that fit these exception. I created separate systems for all these zones.

(FYI, I did receive a review comment on one of these projects where the LEED reviewer asked for a list of all zones and the baseline systems serving them to ensure that they adhered to this exception)

The general idea of having a separate system for these zones is to ensure that the baseline system (5,6,7, or 8) that is modeled for the entire floor is not at disadvantage of higher energy usage just due to a few zones. One way to reduce the number of zones that differ in peak thermal loads is to zone the floor plan more carefully. I lump multiple rooms together according to requirements in Table G3.1.7 to reduce the overall number of thermal zones but again, this may not always be possible.