I looked on those NYS links, but didn't notice anything about the story behind these cars, so here it is Deputy:
In the early 1980's, the NYS Dept. of Transportation purchased, then overhauled and rebuilt a couple hundred box cars for the Delaware and Hudson Railway. They were then leased back to the D&H with the very memorable "I Love New York" paint scheme, as sort of a trade off. The cars were numbered 5000-50199. The "I Love New York" campaign was a promotion to encourage tourism in NYS and was heavily promoted in all media avenues.
I believe the story on the PC green Lehigh Valley box cars is somewhat similar. The Lehigh sold box cars to be refurbished and rebuilt, then leased them back. Only this time the scheme was a more railroad oriented scheme, with the PC green which resulted from the PRR (at the time this happened, now the PC) being a major shareholder of the LV. A few cabooses also showed up in PC green, which die-hard LV fans really disliked.
I'm sure there are other such stories about the real rail lines out there.
Deputy, I know you and I have disagreed a few times - but this time I hope I could help out.