I'm not aware of separate sale on the 3 set cars. I suppose there could have been over run, or maybe someone came across a stash of bodies and doors, and assembled them into complete cars. Given the fact that we are more than 40 years removed from the original production, anything is possible.
It may not be well known that Lionel did some of their own set break ups, offering individual cars from the sets by the case. I have a Lionel order form in my paper collection. Exactly how often they did this, or whether the Coke set was done is unknown to me. If they did, that would explain the boxes.
BTW there is a unique car from the set that has a label for a Tennessee bottling plant. It was in an article in an early Classic Toy trains. I am fairly certain it is the Sprite car. I have never run across one in all the train shows I have gone to.
The Coke set was the brain child of Andrew Kriswalus, who made Kris Model Trains, and owned a business called the Railroad Shop. According to Andy, he was supposed to get the entire run, but Lionel reneged. While he wouldn't be specific, he told me there was a settlement over the issue.
We never spoke about it, but I read somewhere that he took some of the cars and had them over stamped for a bottling plant. But I thought the ones he did were for a local plant in Endicott, NY. I don't any idea who would have done the Tennessee plant. I'm not positive on the over stamping.
I don't have any of the over stamped cars.
I purchased my first Coke set in 1974 from the Railroad Shop. I believe it was $40. I still have the set, I don't think I ever ran it.
I got into purchasing additional pieces because I had mine on display and my iguana climbed up the display shelves and knocked the Fanta car to the floor, damaging it.
The unboxed separate cars turn up with some frequency. The orange Fanta car seems to be the most common. A lot of the Fanta cars I've seen have very poor paint jobs, with lots of crud embedded in the paint.
Maybe they were rejects that someone put together.