There’s no “metal migration” taking place.
Basic material science tells us that a hard/abrasive material will embed itself in the surface of a softer material (in this case, the body of the Pencil) - and this can abrade the surface of a harder material (e.g., the anodised coating of the iPad) as the Pencil slides on/off of the iPad magnetic/inductive charging pad.
This can cause localised surface wear of the anodised finish of the iPad. The marking that you describe on your Pencil body corresponds with the magnetic contact points of Pencil against the iPad. Any abrasive dust or grit that is present when docking the Pencil can abrade the anodised finish of the iPad.
Keeping these surfaces scrupulously clean and dust free - combined with taking care to lift (and not slide) the Pencil from the iPad charging dock can reduce the possibility and occurence of cosmetic surface damage.