Runout WILL cause pulsation. Even though the caliper is free to move, it has mass, and to move it takes energy. The quicker it has to move, the more pronounced is the effect. Force is still equal to mass time acceleration.
And you WILL feel it in the pedal. And by truing the rotor, it will go away.
And when you get some idiot with a torque stick/torque wrench installing a wheel, WILL likely return.