It is really all personal opinion but,
These cars were mass produced just like the ramblers of the day.......many of which were delivered to dealers with trunk lids placed in the back seats because the panel alignments were so bad the factory could not easily fit so the dealers had to install......and back then, the dealers had a pre-approved budget & fixed things like this almost routinely.
Up through the 60's & early 70's, vehicles were not ordered as they are today. Yes, if you ordered package "X" it would come with 1, 2, 3.....but, you could also delete specific items within the package. As an example, our mustang (which has been in the family since it was new), when ordered as a GT, my parents really didn't like "trumpet tips" through the rear pan so the dual exhaust was a "delete" (as shown on the original order papers which we still have) and upon delivery, it was off to the muffler shop for a set of pipes.......a very common practice- which because of this it is not impossible, but I will say it is much more "challenging" to not so much verify something is a factory GT by having all of the items listed, but more difficult to verify it is not..and Ford was not the only one doing this either, a very common practice by the Big 3.
My neighbor worked for GM in Long Beach, Ca back in the 70's, and clearly recalls special order deletes, hand carried orders to install "X" cylinder head on a particular car- he also recalls there was seldom more than a week went by that the cylinder heads didn't change (as far as port matching/sizing/shape)- as it was all dependent on the supplier and that varied by each shipment….or someone wanted their pickup painted the color that was offered on a particular car…..not a problem as long as it was built at the same plant (for an extra charge of course)- which also explains a few very, very ID pates.
While it is a wonderful thing to have a variety of people who have done such exhaustive research on these and other vehicles, and granted, the GT/CS packages were more "standardized" we must also remember that the customer service and deliverables of the time were much, much different than today and paperwork, was, well, not the focus. This has lead to benefit us (especially in Calif) who became exempted from smog testing/cert because of the absence (disposal/non-retention) of documentation of our cars, but in all reality, even if all the paperwork did exist, it wouldn't do little to validate much more than is known today about the cars- because the paperwork was not a priority, delivering what the customer wanted was.
IMHO, if you have the $ and it's burning a hole in your pocket to create a "concours restoration", that's fine, if you just want to do a ground up rebuild, that is certainly appropriate as well. Some will grin, some will sneer......but it's all OK in my book- whatever "makes you happy"!