That looks typical to me. I had a crankshaft offset ground an then had it plasma ion nitride, came back all black, it was a strange type of finish like you said you could effect it by rubbing it but not completely remove it . I had the crankshaft polished on the journals after. If your worried about the stuff on the bearings journals and lobes, you could probably polish with scotchbrite. The stuff on the surface isn't the nitriding, it goes .010-.030 deep.