Manufacturers recommendations usually take precedence over local building codes but you won t know for sure which takes precedence or what those manufacturers recommendations are.
Water heater vent height above roof.
At the hottest point in a gas water heater flue the flue vent connector right above the heater top the temperature is not likely to rise above 350 degf.
Exhaust gases are vented outdoors through a separate vent duct or through a separate chamber of the same pipe this requires a double wall vent duct.
Above the highest point where they pass through the roof surface.
With a direct vent system air for combustion is drawn from a vent pipe that runs through an exterior wall or the roof.
The difference is that a power vent water heater pulls in combustion air from the space around the appliance then uses a fan to propel the exhaust through the vent.
10 4 1 1 vents installed with mechanical exausters shall terminate not less than 12 in.
If it is a natural vent type water heater you can not vent it through the side wall it has to vent above the roof.
It is reasonable to assume that higher in the flue temperatures are much lower.
Direct vent water heaters.
The 2 10 rule states that combustion vents should terminate at least 2 feet above any part of the roof within 10 feet.
All other gas vents shall terminate not less than 2 feet 610 mm above the highest point where they pass through the roof and at least 2 feet 610 mm higher than any portion of a building within 10 feet 3048 mm.
The average being about 6 foot.
Here is the nfp11 codes.