I have never had that, and that video did not make something clear to me. When your bike does that, does it seem to happen on the same spot in the disc? Doesn't seem that way in the clip, but hard to keep up with the wheel rotation. I'd start by marking the wheel when you hear it and checking that.
The next thing would be removing the caliper and making sure the slider pins are clean and greased, so the calipper can can slide on them smoothly. Clean around the piston too, while you are at it. Even if the disc is not perfect, the caliper should be able to move away when pushed (obviously if the disc is truly warped, not just a little out of spec, it will cause other issues when braking).