Preheat oven to 350°F and line muffin tin with paper cupcake liners.
Melt semi-sweet chocolate in a double boiler or microwave, then let it cool slightly.
Whisk together both flours, cocoa powder, baking soda, baking powder, and all spices together.
Beat softened butter and sugar until light and fluffy, about three to four minutes.
Add eggs one at a time, beating well after adding each one in.
Mix in melted chocolate and vanilla bean paste until the batter looks completely smooth.
Stir in pumpkin puree until fully combined and batter turns orange-brown evenly throughout.
Alternate adding dry ingredients and buttermilk, beginning and ending with the dry ingredients.
Fill cupcake liners two-thirds full with batter, leaving some room for them to rise.
Bake 18-20 minutes until the toothpick comes out with a few moist crumbs only.
Cool in the pan for 5 minutes, then transfer the cupcakes to a wire rack for complete cooling.
Beat butter and cream cheese together until smooth and creamy with no lumps left.
Gradually add powdered sugar, pumpkin puree, vanilla, orange zest, and optional food coloring slowly.
Beat frosting until light and fluffy, adding more sugar if you need a thicker consistency.
Pipe or spread frosting onto completely cooled cupcakes using your preferred decorating style choice.