My guess is that since the time frame on this quoted web information is oly about 6-7 years old, and referencing repainting of some ARR Geeps ( smaller types that the ones NS Corp painted). My guess is had they been repaints the figures would have been way North of $40 K per engine.
Since these were new engines, they were delivered in primer; it is probably logical to say NS Corp footed the bill for the custom paint jobs.
Painting would be a single factor; consider the logistics of moving the Heritage Fleet to the locations where they were to be decorated for their service. Fuel, Miles, and Labor, not to mention Logistics to get them where they needed to be to meet the schedules required for the 4th of July festivities at NC Transportation Museum.
NS Corp made it look easy, but you can bet your bippy, that there was a heck of a lot more to that story than Mr.Wick Moorman just snapping hos fingers and wavin