But since the AIR is slowed down within the boundary layer, it reduces the control surface effectiveness, especially during take-off and/or landing approach when the airspeed and AOA may be near stall.
Also in those circumstances the conventional aileron that moves upward is acting in the disturbed flow from the wings upper side, whereas the one that moves downward increases the drag, which may lead to adverse yaw.
The "Junker" aileron/flaps type are often used on aircraft designed for STOL.