Besides, the autopilot can handle all of the throttle inputs

What they're saying in this article, is that as long as the aircraft stays within a certain area within range of another aircraft, the benefits will still be applicable. Maybe to a slightly lesser degree than if they were a hundred or so feet apart, but still there.
Doesn't matter who's controlling the throttles, the basic mechanics are still the same, and even with a "cleverer" computer, you'll still have more variation in engine power settings, and hence probably lose any potential benefits.
Then the matter of traffic control, or lack of it, over the Oceans, has the be thought of. With aircraft crossing in 60 mile wide lanes, avoiding weather or dealing with in flight emergencies would be a nightmare. Mind you, for navigation equipment failures you'd be allright!
