Preheat the oven to 350 degrees F. Line a standard twelve-cup muffin tin with paper or silicone liners or lightly oil or mist it with cooking spray.

To make the cupcakes, put the water and flaxseeds in a medium bowl and whisk to combine. Let rest for 10 minutes to thicken. Add the milk, oil, and vanilla extract and whisk until well combined. Put the almond flour, rice flour, sugar, cacao powder, tapioca starch, baking soda, xanthan gum, baking powder, and salt in a large bowl and whisk to combine. Add the flaxseed mixture and whisk until well combined.

Fill the prepared muffin cups using a ¼-cup ice-cream scoop or measuring cup. Bake for 20 to 22 minutes, or until a toothpick inserted in the center comes out clean. Let cool for 20 minutes, then transfer to a rack to cool completely.

To make the frosting, put the margarine in a large bowl and beat with an electric mixer or stand mixer on medium speed for 1 minute. Add the powdered sugar, cacao powder, milk, and vanilla extract and beat until light and fluffy, 2 to 3 minutes. Spread the frosting over the cooled cupcakes with a table knife. Alternatively, fill a pastry bag with the frosting and decoratively pipe it onto the cupcakes.