I don't think your information regarding NRA instruction is entirely accurate. Monday night I attended a handgun proficiency course at the local shooting range. The instructor was NRA certified, and I asked him this very question. He gave me the same answer you just gave above. Perhaps he was only speaking for himself, but he didn't say that the NRA position was any different.
It's possible they've revised the instructor curriculum. In the NRA Basic Pistol course I took, they taught hammer down on empty chamber for revolvers. I'd have to check if their companion textbook says the same thing. I figured they just kept the old method so that people who are not savy about such things as transfer bars wouldn't go putting a live round under the hammer of Grand-Dads Colt.