The marks that you illustrate on the iPad is localised surface wear of the anodised finish of the iPad. The dark patches on the Apple Pencil body correspond with the magnetic contact points of the Pencil to the iPad inductive charging dock. Any abrasive dust or grit that is present when docking the Pencil can abrade the anodised finish of the iPad.
Basic material science tells us that any hard/abrasive material will embed itself in the surface of the softer material (in this case, the body of the Pencil) - and this can abrade the surface of the harder material (the anodised coating) as the Pencil slides on/off of the iPad charging pad.
Keeping these surfaces clean and dust free can reduce the possibility of cosmetic surface damage.
The anodised surface finish on your iPad, where damaged, is now a missing surface layer. For the Pencil, as the contamination is embedded in the body of the Pencil, it will likely be difficult to remove. Whatever you do, don’t be tempted to use any abrasive material to clean the Pencil body, as this material will itself be embedded in the softer plastic of the Pencil.
In summary, prevention is the only remedy for this type of cosmetic surface damage.