I have also felt the hot brake pulse and suspected I had warped them. They have always had a good pedal and performance. Some of the boosters feel very different between vehicles so I don't expect it to feel the same. In my case, the pulse changed back to smooth as glass as the brakes cooled. Why not get both vehicles out and get them up to the same speed and do a full stop on a mark and see if it is just pedal modulation under hot conditions but your performance is not hurt. The Z06 should be a shorter stopping vehicle.