What you say may be the actual case but it makes it very difficult to prove a restoration is back to its factory/showroom condition. If they ran out of chrome lids it might be evidenced by painted lids after a certain build date.
What you say is true but not always relevant. The term "restoration" means different things to different people.
Did the factory build cars using the wrong parts some times? - Yes!
Were they supposed to do that? - No.
Restoration for a particular car can mean that a car is returned to it's original "as delivered" condition with any non-spec parts OR does it mean "returned to normative practice" with all the correct specified parts.
Normative practice is more like what the factory should have built given the time and proper specified parts. "As Delivered" might mean the car had some parts that were not exactly per spec but that is what that particular car had leaving the factory.
If you do not have any STRONG physical evidence IN YOUR HANDS to show others that a particular car was delivered with parts that were not correct "normative practice" you are shoveling sand into the ocean. There is no real reason for anyone to accept that these incorrect parts are original for that car.
The car in question has numerous aftermarket replacement parts all over the engine bay. it is not possible to say with any certainty how much of this example is "original to the car" but we can determine if the parts and pieces are aftermarket or "normative practice" from research, casting numbers and date codes etc. Thats about all we can ever know.