1. Preheat oven to 350°.
2. To prepare cake, weigh or lightly spoon flours into dry measuring cups; level with a knife. Combine flours, cocoa, baking soda, xanthan gum, and baking powder in a medium bowl; stir with a whisk.
3. Combine granulated sugar and next 4 ingredients (through food coloring) in a large bowl; beat with a mixer at medium speed until well blended. Add flour mixture and 3/4 cup water alternately to sugar mixture, beginning and ending with flour mixture.
4. Spoon 2 tablespoonfuls batter into 24 mounds 2 inches apart onto baking sheets lined with parchment paper. Bake at 350° for 12 minutes or until cakes spring back when lightly touched. Cool completely on pans on wire racks.
5. To prepare filling, combine 1 cup powdered sugar and next 4 ingredients (through vanilla) in a medium bowl. Beat with a mixer at medium speed until light and fluffy. Spread about 1 1/2 tablespoons filling onto bottoms of 12 cakes; top with remaining cakes, bottom sides down. Dust both sides of whoopie pies with 1/4 cup powdered sugar just before serving.