In a medium saucepan, cover the beets with water and bring to a boil. Add a generous pinch of salt and simmer over moderate heat until tender, 40 to 45 minutes. Drain and let cool completely. Peel the beets and cut into chunks, then puree in a food processor until very smooth. Measure 1 cup of the puree and reserve the rest for another use.
Preheat the oven to 325°. Grease three 9-inch round baking pans with nonstick cooking spray and line them with parchment paper. In a microwave safe bowl, melt the chocolate at high power in 30-second intervals; stir until smooth.
In a large bowl, sift the cake flour with the baking soda, nutmeg and 1/2 teaspoon of salt. In a stand mixer fitted with the paddle, beat the butter with the granulated sugar at medium-high speed until fluffy. At medium speed, beat in the eggs one at a time until light and fluffy. Beat in the 1 cup of beet puree along with the melted chocolate, buttermilk, vanilla and food coloring (if using) until no streaks remain. Scrape down the side of the bowl, then beat in the dry ingredients in 2 batches until just incorporated.
Spread the batter in the prepared cake pans and bake for about 30 minutes, until a toothpick inserted in the center of each cake comes out clean; rotate the cakes from top to bottom halfway through baking. Transfer the cakes to a rack to cool completely.
Step 5 Meanwhile, make the icing
In a stand mixer fitted with the paddle, beat the cream cheese with the butter, vanilla seeds and salt at medium speed until smooth. At low speed, beat in the confectioners’ sugar until incorporated, then beat the icing at medium speed until light and very smooth. Refrigerate until lightly chilled and firmed up, about 30 minutes.
Unmold the cakes and peel off the parchment paper. Invert a cake layer on a large cake plate and frost with one-fourth of the icing. Place another cake on top and frost with another one-fourth of the icing. Top with the remaining cake. Frost the outside of the cake with one-fourth of the icing and refrigerate until the icing is firm, about 1 hour. Frost the cake with the remaining frosting and, using a spatula, decoratively swirl the top. Refrigerate the cake until the icing is set, about 45 minutes. Cut into wedges and serve.
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