Localised hotspots on the disc with pad deposits can also cause the iron crystal structure to turn into martensite.
This is an extremely hard type of iron which will react differently to the pad moving over it as far as friction coeficient goes and also not wear at the same rate as the rest of the disc giving a pulsing/juddering brake feel.
If this is indeed the case then it should show up if you try to have the brake discs skimmed/turned as there will be areas where the lathe tool will have a much harder time to take off the material. If it's deep enough then the disc can't be saved.
CL pads don't need a bedding-in process as long as conventional pads as they do not have a binding agent that needs to first be 'boiled off' to get the proper friction surface exposed (which is why the normal 'brake from xxx to yyy and repeat for zz times over a period of qqq' advice is given), but like any pad they do need a short bedding-in process until the pads (both inner and outer) have equal and consistent pad contact across the width of the disc.
Any 'stripes' or voids in the contact area will mean the disc will heat up un-evenly if it's heavily used promoting flexing of the disc because of differential expansion. If bad enough then the dics can permanently deform from the stress and needs to be turned down to be even and smooth again.
Bye, Arno.