Preheat oven to 350 degrees and line two muffin tins with paper liners. Set aside.
In a small mixing bowl, sift together coconut flour, oat flour, potato starch, sorghum flour, xanthan gum, baking soda, and salt.
In a larger mixing bowl, cream together eggs, sugar, honey, peanut butter, and shortening until smooth and pale in color. Add vanilla and milk. Beat until combined. Add flour mixture and mix until incorporated. Add Greek yogurt and mix until combined, scraping down sides of the bowl. Beat mixture at medium speed for three minutes.
Fill muffin tins 1/2 way full with batter and bake, one pan at a time, for 18-22 minutes (rotating after 18 minutes) until muffins are golden brown and spring back at the touch of a finger.
Remove muffins from oven and let sit for 2-3 minutes on cooling rack. As soon as you are able, quickly remove muffins from tins and allow to continue cooling on cooling rack.
For chocolate topping, microwave chocolate chips in a microwave safe bowl at 50% power or defrost for 30 seconds. Stir chocolate chips for at least a minute to melt chocolate. Microwave in additional 15 second intervals, stirring for at least a minute in between, until all chocolate is melted and smooth.
Holding bottom of muffins, dip the tops in the melted chocolate and sprinkle with chopped peanuts. Refrigerate muffins until chocolate hardens, about 5 minutes. Remove from fridge and serve at room temperature.