This question always puzzled me.
The engineer has to know what he says, of course. But let me explain my "theory".
I always thought that induced drag (the one responsible for the wake turbulence) for a given lift depended on how this lift was was distributed on the wing planform. If most of it was in the root, like in airplanes with long span, or with eliptical planform, or with some taper ratio, then induced drag was less. Because the "leakage" of air at the wingtips was less.
All wings (or all I know, at least) have flaps in the root area and ailerons near the tips. If we maintaing the flight path after extending flaps, lift will be the same (after the ballooning) but lift distribution will be now more concentrated in the root, therefore reducing induced drag. This makes sense, Doesn't it?
But then, why don't we keep the flaps down all the way as he suggests?
Because when flying at high speeds parasite drag is the problem, not induced drag. And with the flaps down we have lots of parasite drag. This makes sense, too.
What do you think, guys?