A flywheel grinder is basically a small Blanchard grinder without a magnetic table. Flywheels / rotors are bolted down with a piloted center. To do the opposite surface you have to flip the rotor. To the chatter, yes you can if you push too hard with a big cut, otherwise no issue. Instead of segment stones like a Blanchard they use cup wheels of different abrasive media. Media choice is dictated by the material being ground, steel, cast iron, etc.
First time I have seen the JHM rotor setup. I don't know if all they do is machine the hat and use someone else's rotor or cast their cast their own discs. Chances are they purchase rotors from one of the known suppliers. These look to have an even pattern, bad pattern but even. That shows that the rotor is running true. The last shot of the resurfaced rotors on the car shows that the pads are not making a full contact with the rotor. Hard to say the root cause from a picture but it is a pad or caliper issue not the rotor creating that pattern. I am assuming that the pads are not narrower since they had full coverage on the previous picture.
Corbett, Other than a unidirectional grind to assist in bedding, (just my preference, turned rotors bed in just fine much of the time) I would try some different pads. You are getting very uneven pickup. In theory, the purpose of bedding pads imbeds a layer of pad material into the rotor. The pad creates friction against this layer. If I saw this pattern the first thing I would do would be to change from an organic pad compound to a ceramic material. Since you are already running a ceramic compound I could only guess that a brand change would be an option. Just never had good luck with hawk pads, but again a personal observation, you mielage may very.It would be interesting to do a back to back with the same pad compound on an OEM rotor and these JHM ???
Rick