I tend not to use it but I have wondered how it might help CTR. For instance if you had an average position of 1.5 and knew you got a significantly better CTR in position 1 then 2.
You could setup ad preference to 1, thereby saving you any impressions on slot 2 and increasing your overall CTR, thus decreasing your minimum bid.
Now, I vaguely remember this feature being discussed in the AdWords learning center tutorials, but I never paid much attention to it. From what it seems like, I believe you set a preferred cost per click as opposed to a maximum cost per click. Is this the same thing as preferred ad positioning you mentioned?