One possibility - landing flap is usually pretty draggy, and the spoilers/lift dumpers are usually destroying most of the lift incrememnt due to the flaps (since they are usually aligned). So retracting flaps might have only a marginal benefit in terms of weight-on-wheels and braking, and actually degrade the aerodynamic drag. i.e. less drag with flaps retracted, which is bad for stopping of course
The complexity of another automated system to certify probably isn't worth it.