Where they apply depends on the equipment. API air coolers take the allowables around the flage face as you said, but talk to any vessel guy about allowable nozzle loads and you'll find they take the allowables at the nozzle / shell interface as that is the critical point [PD5500 App G / WRC] to them. If the allowables loads are on the flange, they need to allow for the moment arm of the nozzle neck with lateral shears.
You really need to be clear with the vendor/client where these loads are to apply.
For instance the outlet of a column typically consists of a bend directly on the bottom dome, and then a long length of pipe to take the nozzle flange outside the skirt. You cannot apply the same level of loads to the flange of this nozzle as you can to the flange of a shorter nozzle [of the same size] fixed directly onto the shell.
Most local load calculations I've done [PD5500 App G & EN13345] only calculate shell stresses for axial force, and circumferential and longitudinal moments. These three components tend to give rise to bending stresses within the shell and these are the critical points for a pressure vessel.
Both codes largely neglect the three shears [circ force, long force and torsion] as these are usually of negligble magnitude [PD5500 does give equations if you feel they are high].
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Kenny Robertson