FWIW, you should baby it for a week or so whenever you change pad compounds (e.g. ceramic to metallic) because you want to get rid of the old pad material layer before bedding in the new pads. You don't want two layers of different materials on the rotor, which is what bedding different compound pads immediately will do.
Of course, as already pointed out, this isn't necessary for most street pads, which should be bed immediately
OP, if the dial indicator says the rotor is out, call up Z1 and explain that it appears as though you got bad rotor. Also ask them what the starting width is and check it against yours so you can demonstrate very little wear along with the mileage on them. Explain that you weren't able to bed properly due to the defect. They are very big in this community and if its a manufacturer defect, they should take care of you.