These are not burns, or marks caused by heat.
Your photos illustrate localised surface wear of the anodised finish of the iPad. The marks corresponds with the magnetic contact points of your Apple Pencil. Any abrasive dust or grit that is present when docking the Pencil can abrade the anodised finish of the iPad - this occurring gradually over time.
Basic material science tells us that hard/abrasive particulate material (commonly occurring in environmental dust) 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.