Misunderstood problem with iPad pro (Pen magnet destroys the case?)

The marks illustrated in your photo are due to localised surface wear of the anodised finish of the iPad. The illustrated marking corresponds with the magnetic contact points of your Apple Pencil shown in the second photo. Any abrasive dust or grit that is present when docking the Pencil can abrade the anodised surface 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 can then abrade the surface of the harder material (the anodised coating) as the Pencil slides on/off of the iPad charging pad. Hard ferrous particles will obviously be attracted to Pencil's magnetic contact points - and will be the cause of corresponding localised damage to the iPad's anodised surface.

Keeping these surfaces clean and dust free can reduce the possibility of the illustrated cosmetic surface damage.

The cosmetic damage that has occurred cannot be repaired short of replacing the unibody-chassis upon which the iPad is constructed - effectively replacing the iPad. While unattractive, the cosmetic damage will not impact your iPad's performance.