From the original cars I've seen and owned things like different than regular production optional hubcaps would have been handled at the dealer. Since the hubcaps were not installed at the factory (due to thief concerns) but once the car arrived at the dealership - as were the antennas. In that case to reduce the chance of damage
Caused allot less confusion that way and it also allowed for the dealers to "upgrade" (and change) a buyer for fancier hubcaps if needed to make a sale IMHO. Know of a number of cars that had the hubcaps changed at the dealership to make a customer happy - one a 70 Special order paint convertible I owned years ago. The original woman buyer did not like the fake wire hubcaps that was available and had the full size real wire hubcaps installed instead. Window sticker showed them but the shipping invoice did not. And since the car was a special order paint car that the woman ordered and waited for, we can assume that the hubcap change was not something (in this example) that was just done to make a sale of a car already on the lot. And that was supported by her story
As for "special ordering" other items the answer IMHO is sort of yes or no depending on allot of things. During 69 & 70 you had limitations by what was legal (emissions comes to mind) and what could or would be warrantied. SPecial colors was the most popular special thing to do to these cars and it was relatively cheap. Of course with the access to the Ford data base allot of claims by owners (in the past) of special order options faded away.
Think allot of these out of ordinary things got handed (if true) at the dealership level though I'm sure there were a few with connections that some oddities but that percentage of overall production very very small.