The roofing permit is asking roof mean height?
I've always used from the ground to the ridge.
Miami-Dade seems to be asking something else.

Anyone know what scupppers are for roofs?
I'm assuming they are drains for flat (low slopes) yes no?

Mean height roof height is not the total height (ground to ridge). Its basically taking a gable roof and cutting it in half.

If your building is 10' tall (floor to wall height). The roof is 6' from top plate to ridge. Your mean roof height would be 13'. It almost like taking a structure with a peaked roof and making it a square box. If I could draw on here it would be easier to explain.

As for roof scuppers, they are used in flat roof/ built up roof systems to divert water. Usually to divert water into gutters.