Of course it's part of the whimsy of toy trains.
That the Atchison Topeka and Santa Fe RR would've painted any of their crack passenger trains BLACK for the trip across the Southwest to/from LA...especially in the summer months!...is ludicrous. Baking the passengers in a rolling oven would not be part of a memorable trip, methinks. Air conditioning systems on mid-century passenger trains were a high maintenance item needing all the help they could be given for passenger comfort.
BTW, there was an article in an old issue of Classic Toy Trains on the origin of the Lionel 'Blackbonnet' Santa Fe scheme. Update: Found the issue...October 2002, page 44. As others have mentioned, it had to do with a catalog artist's conception from a photograph. It was a real lulu of a faus pax...destined to whimsical hobby history...hysteria!...forever, obviously.
Hey, one of the nice things about this fantasy scheme is that there has been little of the usually ubiquitous argument about the 'correct' black paint used by the manufacturer(s)!
KD