At the Rochester & Genesee Valley RR Museum site, the NYC System Historical Society has an illustration of a NYC MDT reefer that's a dead ringer for the Lionel NYC freightsounds reefer (orange sides, red roof and ends), so the colors appear correct. The build date on the illustration is 9/56, but they were also built after that. (The Museum has two MDT reefers in their collection.) Research shows that many MDT reefers, perhaps most, were painted the same way, reefer orange with red tops and ends.
These reefers were used well into the 60s; in fact, in 1965, the MDT still had 10,112 reefers rostered. The KarTrak bar codes were required by the AAR starting in '67, and may have been used in some cases before then. The system was abandoned in '77 due to technical problems. It seems entirely possible, likely even, that NYC MDT reefers had KarTrak bar codes at some point.
Bottom line: the Lionel car appears completely prototypical.