Our company has visa guidelines (for both personal and business travel). "The [] Team, in consultation with the Ministry of Public Security of the People's Republic of China, has developed these guidelines for holders of U.S. Passports. However, you should always be prepared to make changes to your itinerary in the event of necessity."
They then talk about the transit visa and indicate, essentially, that the airports listed on the boarding pass are controlling. They then talk about unscheduled landings, etc. However, based on those guidelines (I have no familiarity with the transit visa other than the fact that I've used it personally before) a scheduled landing at NRT qualifies as a third country regardless of the length of the stop (unless there's something special about NRT, but it doesn't say anything about that).
I'd believe these over any airport agent considering last time I went to China with my wife who is Taiwanese, the GA was claiming that she didn't have the appropriate documentation. My wife, being Taiwanese with family living in China, knew exactly what documentation was required but the GA kept insisting that she "[didn't] know what [she was] talking about." I haven't wished bad things on many people, but that GA is one of the people I was really hoping would get fired (more based on her handling of the situation than lack of knowledge).