Perhaps the cart might be getting ahead of the horse...
Efficiency, in the sense related here, is about the combination of aircraft and propulsion. Taking the formation case, the leader may fly at an efficient speed, the wingman's speed will vary around that, and some of his fuel burn at least will be a consequence of the time spent not flying at the leader's efficient speed.
Yes, acceleration and deceleration will mean less efficiency, but a given aircraft will use less fuel cruising at a given speed with a good autothrottle than cruising at a given thrust setting and allowing the speed to vary.