Over time they may wear-in and smooth-out. The rotors may be slightly warped by your description of those perpendicular marks.

These things are finicky for sure. Breaking in a new rotor is an important step and there is a process one needs to go through to do it right and avoid pulsing brakes. I'm not saying you didn't do it right but these things are really finicky. Quite frankly I don't like them and only ride them on one bike of mine, a mountain bike.

Try the cleaning with denatured alcohol and a light sanding of both pads and brakes and Google breaking in brakes to see the process. FWIW my first foray into these things came up with the same issues you're having. After going through the proper process with new pads and rotors they are smooth as silk.