UCLogic ...
As a rough guide .... ANY configuration/change from the "standard aircraft" (as described in the Airworthiness Certificate supplied by a manufacturer) requires mention in the aircraft flight manual which IS a legal (and controlled) document.
Any modification, including an STC once incorporated HAS to have the applicable supplement incorporated in the aircraft flight manual AND it is the responsibility of the aircrafts maintenance organisation to see that this is done. (It might affect the a/c W&B for example).
Technically an aircraft cannot be
signed out as "servicable" unless this has been done. It is then the pilots responsibility to ensure that the aircraft he accepts for flight is acceptable and that he is aware of the a/c configuration.
All of which may have consequences with regard aircraft insurance etc etc. and of course is subject to the requirements of particular licencing authorities.
Cheers