From what I can gather in the article they are talking about medium haul aircraft doing the routes. Now those, even if they use less fuel can only hold half the pax of a 747-400 so they will be less efficent.
I did some calcultaions for a 747-400 Full Load on a rudimentary flight planning program. (Actually designed for 744 PS1.3 Precision Simulator) Not 100% accurate I know but illustrates a point.
The times map had London-Bahrain-Delhi-Singapore so I used that route.
London Bahrain- 57 Tons Trip Fuel
Bahrain Delhi 30 Tons
Delhi Singapore 47 Tons
Total of 134 Tons
Another one I tried was one stop
London Baharin 57
Bahrain Singapore 72
Total of 129
Now the Total direct, these are all Great Circle, No Airways / Winds etc, was 133 Tons so the only saving would be going one stop but even then 4 tons doesn't seem to be worth the effort.
If anyone has the time to work out any calculations on a real life flight planning system for a 747-400 to include winds etc, then it would be interesting to see whether the Times article would be valid for a 747-400