Ver-ry interesting.
It's possible that the UP had developed an imbalance of power and had to get some of those units back to the other end of the district. (I have a photo of a 4-car passenger train with doubleheaded Pacifics - same situation.)
As for 2001, when it was hauling The Flame it operated with a special Flame car and a couple of business cars.
Tarp-covered gondolas? Was it sugar beet season? There are any number of reasons for covering gondolas to either keep lading in the cars or keep contaminants out. Modeling them would make for an interesting game of, "What's in the car," for visitors.
Chuck (modeling Central Japan in September, 1964)