This is a very good question, and I'm glad you asked it.
The answer is VERY subjective, because car shows are not an exact science. Having a built sheet--and/or Marti Report with your options on the car--and on the list-- is the best way to go.
However--there were many "factory" options that were also added by the dealer. Some with the exact same parts--other with something bought by the dealer, or from an outside manufacturer that sold "kits" to dealers to add to cars to sell them. "IF" you wanted a Shelby Aluminum FE intake put on, the dealer would order it, and put it on, but you'd be advised that it would probably invalidate your Ford warranty.
There are lots of options that as long as they are "period", and, WERE authentic, separate options that the dealer did put on to cars, then I say go for it. Cobra Dress up Kit, Rear Speaker Grilles, Rear Window Defogger w/switch, Vinyl Top, Dual Exhaust, add-on headrests, fender trim, etc...are all add on stuff you could get.
To be blunt about it--you get a lot of politics at car shows about whether something was or was not "originally" on the car. What if the original owner added a (late) '68 Hood tach 3 months after he bought the car?
It's not so much what is right or wrong about this. It's whether it makes you happy--on YOUR car. If you feel strongly about adding an option--and you research it, and it's 100% all there as a dealer put it on, then I say go for it. Besides--I like "educating" these know-it-all judges at car shows with this stuff.
IF you add a factory-only option, like a deluxe interior (never a dealer option), it will be difficult to "prove" it if you have a Marti Report out there saying otherwise.
On the other side--I' know of an owner of a stock '68 coupe that had their undercarriage "undercoated" completely, despite the fact it was a San Jose car--which didn't get all that much coating. They did it to win a "national Mustang Club" show, because they based their rules on East Coast cars from the NJ plant that undercoated their cars much more. So..go figure.
It's not an exact science--but it could be, if those who do these rules sat down and figured it out. All the data is there. Rules today are waaay too subjective to favor the influential.
I say do what makes you happy.
Paul Newitt