You could well be 100% correct.
A definitive answer would require access to some historical data on the reasons for the introduction of the gross to net decrement .. unfortunately, this I don't have and can never recall having seen .... probably could hunt it down in the historical FARs, either explicity or by implication, but that would take more spare time than I have to spare...
Looking at the current FARs, for instance,
(a) 25.115 (as an airworthiness design standand) prescribes the decrement but makes no reference to obstacle clearance.
(b) 121.189 (as an operational standard) relates the NFP to obstacle clearance.
Perhaps your colleague and you are both correct but looking at the problem with different sets of spectacles ...