I am just trying to find some logic. Airbus has some specialities like flap lever has straight forward five postions but actual slat/flap surface combinations are different. So perhaps in unusual situations may be the warning also act different. Like the GPWS too low flap only comes from flap, the slat plays no part. So if flap cannot go to three we are asked to switch off the mode itself. In this ATHR overspeed protection in normal situation flap lever(barber pole) is not the factor to trigger ATHR overspeed protection. But the flap auto retract may be making the difference or the system doesn't have time to trigger ATHR during the short duration of retracting slat. By the time it retards thrust the situation is over but warning is triggered.