To add my 2 cents worth, I am an A&P; IA; and DAR. If a major component on the aircraft is of a certified nature and failure of which would make the aircraft unsafe, yes, they apply. For instance, if the data plate on the engine is a TC data plate, and there is an AD to "Reflamagate the hypodusinators prior to further flight", yes, it does apply! However, if the data plate is modified to reflect the experimental nature of the item, then it "may" not apply. However, I think a better way of looking at it is to put yourself in the position as a Repairman for that aircraft, and did not "reflamagate the hypodusinator", and there was an accident because of that failure, and you are sitting in the courtroom, and you are asked why you stated the aircraft was in a condition for safe flight, when the manufacture of a major component of that aircraft stated otherwise, "YOU CAN BEAT THE RAP, BUT YOU CAN'T BEAT THE RIDE!!". Also, the insurance company may have a very conservative attitude toward safety.
Regards,
Gary