Since Antinos didn't post the answer to this phenomena, so I asked a person that have done some consultant work for GCI during the Twister film day about it (since Twister brake run also is banked).
The reason for it is to be able to increase the brake force of the magnetic brakes to put it in a simple answer. How you might wonder then, well wooden coaster track are built by hand with less tolerances than steel coasters and to make sure that trains won't get stuck they add a little extra play between the wheels and the track. This play means that the train (and brake fin) can move a bit side to side and due to this they have to widen the slot between the magnets so that the brake fin won't hit it, widening the slot will reduce the brake force.
By banking the brake run the train will always be running along the same side which will put the fin at the same location so that you could use a narrower slot and get a better braking performance even if the wheel gaps are pretty big...
