... in this instance I am not asking Esoteric to be responsible for APL’s work. APL modified the DAC circuitry, the problem is in the transport which APL did not modify.
Perhaps, although Esoteric has no way of being sure of that. It’s also possible that modifications to the DAC could have an affect on the Esoteric’s power supply, which could also conceivably affect the transport. So you are indeed asking Esoteric to assume some responsibility for APL’s modifications. You should know that many audio manufacturers have the same policy and some - such as Audio Research - as especially transparent about it. I think that partially explains why modified components usually fetch less on the used market than a similar unmodified sample.
I fail to see how an Esoteric dealer could solve this issue. The dealer would necessarily need to rely on support from the manufacturer, and their national service representative.
As his customer, your dealer has an interest in keeping you happy. One of the most valuable roles a dealer can fulfill is being the intermediary between a manufacturer and end user and asking him to assist in obtaining a part or schematic is perfectly reasonable. In the same vein, your dealer is effectively a customer of the distributor or manufacturer, so they have a reason to keep your dealer happy by helping him with his customer.
The world of audio is a rather small club and a lot depends on relationships. Good customers usually get the best service, ime @johnax.