I agree, but ...

The article makes it clear that they didn't really have 12 hours for touring. They checked into a transit hotel to freshen up and leave their bags. By the time they actually headed out for a visit, it was 9:00 am, with their departure scheduled for 4 pm. That means they only actually had about 5 hours if they returned to NRT 2 hours before departure. In that case, I think Narita-shi was probably a safer bet. They did some window shopping along the shopping street, visited the temple and had a meal. Actually a pretty good use of the time and less stressful than trying to go into Tokyo for what would have been only 3 or 4 hours. If they had foregone the transit hotel and just dumped luggage at the baggage counter, then I think 8 or 10 hours in Tokyo would have been a better use of the time.