Damage modeling is the weakest part of AH. It has always been.
Asking for a damage model instead of auto retract is in principle a request for more realism. In practice it is a request for less. IIRC, HT stated that they have no good way of modeling such a thing as flap over speed/stress damage. Not only this is more complicated than the current damage model can support, there is also an extreme lack of data to model this by.
HTC has to make a choice: Model the pilot's hand retracting the flaps, even involuntarily (aka disciplined pilot flying by the manual), or start guessing and make up data required for a quasi-realistic damage model for the flaps. It is quite clear what they consider more 'realistic'.