A37575, I am bemused by the situation which you describe. It is difficult to respond without understanding the authority’s position and particularly the details of any assumptions made.
Each operator has a right to an opinion, but if the situation is as described (and I’m not overly surprised) then this is a very sorry and potentially frightening situation for the industry.
It would be difficult to justify instrument flying competency from just one (manually flown) approach. However, if this is acceptable it could imply that only abnormal circumstances need be considered where higher accuracy procedural performance is sacrificed – but the operation must still be safe with respect to terrain etc. Such situations might require declaration of an emergency when flying IFR manually or only with FD (I have heard of that before).
Reduced instrument flying skills mean much more than the ability to fly; they are involved in situation awareness and decision making which are essential components of operations with or without autos / FD.