The Maximum Ceiling Height setting (highest overall floor to ceiling height) contributes to the ventilation calculation, which is applied to every external wall and opening, so it's important to be accurate.
It doesn’t matter which zone type (conditioned or unconditioned), as it uses the maximum ceiling height instead of assuming the eave height above ground is correct.
It essentially allows assessors to inform/override system and background calculations in the event of a raked/cathedral ceiling or any other unexpected design feature.
By example, in AccuRate you set up each zone with a maximum ceiling height and the system uses the highest one. BERS assessors enter the information once.