Like many of those things that Harley calls "normal", it's only on some bikes and some parts. To me that's not "normal", it's an indication of just how sloppy their designs and quality control are. The floating rotors on my earlier model bikes never made a clunking sound, so it's not something that is inherent in all floating rotors.
I guess if someone wanted to make a point, or just satisfy their curious mind, they could substitute the plain rotors from a standard model without changing anything else and then see if the noise disappears. Probably not worth the effort, however. I think this is just one more of the many, many irritants that a Harley owner has to learn to live with as part of the privilege of owning one of Milwaukee's finest. (Actually, I thought Milwaukee's finest came in a bottle or keg.)
Jerry