I think it's different for every city. In Austin mechanical penthouses, rooftop stair towers and even main roof parapets are exempt from height variances the developer is seeking. The only cases where those rooftop elements are required to obey a set height restriction is when the building is within a capitol view corridor or if it fronts the river or one of the two creeks in downtown. Otherwise, those elements don't count toward the extra height they're seeking. They don't even count that height when stating the height of the building and sometimes the elevations don't even show the heights to the very top. The only height the city cares about here is the main roof height. However, that doesn't mean that every building height you see for Austin on SSP, for example, is lower than the actual height, because I still measure and count to those points. Most of the time the elevations do show mechanical penthouses and spires, etc. Otherwise, if for some reason I'm just not able to find the height through the city documents, I'll measure it with Google Earth, but I've only had to do that for a handful of buildings.
EDIT: I didn't realize OEAAA was referring to the FAA. I have relied on them from time to time, but I've found their heights sometimes to be different from what was listed on the site plans/elevations filed with the city. I tend to not go with the FAA's numbers as the final height. They are an ok source for getting an idea of the scope of a project, but I wouldn't rely on them as a main source.
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