I always do a break in on my brakes. I want to make sure everything is working to it full potential and to find any issues. Making sure that the shoe face is fully in contact with the rotor or drum.
This was very important to do when you have drum brakes, as the shoes will not have good contact with the drum. Also with drum brakes, you must do several forward and reverse stops the work the automatic brake adjusters after manually adjusting the brake shoes and breaking them in.
With rotors the pins, slides, calipers, and mounts wear, which can cause the brake pad face to not be squared up to the rotor face. That causes the pads to not make full contact until they are worn in and that will increase your stopping distance