One of my jobs as an engine engineer was to respond to customer problems that cropped up in the field that could not be solved at a lower level. I can tell you that while everyone likes to think the factory doesnt make substitutions or replacements, it happened, and it happened in some weird ways. You would find all kinds of things in an engine that werent supposed to be there, carbs distributors and so on, so the thought that each engine and trans and so on is waiting on a list somewhere for a certain car is not right. While it might be the goal, and Ford certainly had a long history of doing it they still made mistakes, engineering changes, inventory changes, mods, running changes order mixups,shift changes, and just plain serendipity all pile up to make it interesting.
If your thinking that each and every engine is built for a certain car ,,it wasnt,,, if your thinking that every engine was built to the current configuration,,it wasnt. If the engine factory had extra 390 heads in a pallet that got moved, they used them, because to not use them cost a lot of money.
I think what your talking about 6T8-390Gt is an assembly plant where the lines run cars based on the order system, of course and dont run that particular car if they dont have the parts. But an Assembly plant is the end of the line of a lot of plants, Ford manufactured its own engines and that plant didnt wait for an order to cast, machine and build up an engine, they had to be up and running at day one of production. You might have several vendors for rubber tubing but you have only one casting plant and only one carburetor plant and so on, those parts come together long before your car is ordered. They recieve running changes all the time and those changes change parts and so on, its a very complex operation and it breaks down in some instances, its remarkable how well they do it however.