The increased allowance for anti-skid is because of degraded braking. By factoring it onto the flap failure, you are increasing the penalty for anti-skid above what was in the makers mind. Therefore in my opinion, you add them separately and not factor one on top of the other. That is what I would do. There are tables for defects in the QRH, and if the maker wanted increased penalties to apply, then there would be a combined failure mode given.
I would say I think it unfair to be hammered with that in the simulator!