There are few desserts that provoke so many comments about "decadence" as a truffle cake. Serve it slightly chilled, with a glass of cold milk as an innocent accompaniment.
Heat oven to 350 degrees. Arrange two racks in center of oven. Line bottoms of three 9-by-2-inch buttered cake pans with parchment; butter again. Dust bottoms and sides with cocoa; tap out excess. Sift cocoa into a medium bowl; stir in 1/4 cup plus 2 tablespoons boiling water until smooth; gradually whisk in milk. Set aside to cool.
Sift flour, baking soda, and salt into a bowl. Set aside. In an electric mixer fitted with the paddle attachment, cream butter on low until fluffy. Gradually beat in sugar, scraping down sides twice. Beat in vanilla.
Add eggs, a third at a time, beating after each addition. With mixer on low speed, alternate adding flour mixture and reserved cocoa mixture a little at a time, starting and ending with flour mixture. Divide batter evenly among prepared pans; spread with an offset spatula until level.
Bake 20 to 25 minutes, rotating pans if necessary, until a cake tester inserted into the center of each cake comes out clean. Let cool in pans set on a wire rack, about 15 minutes. Remove the cakes from the pans, and return to rack to cool, tops up.
Trim cake layers until level. Place one layer of cake on a cardboard cake round. Spread about 1 1/4 cups whipped ganache on cake; top with a second cake. Repeat. Spread remaining whipped ganache evenly over top and sides of cake to seal in crumbs and form a smooth surface. Chill until crumb coat is firm, about 30 minutes.
Place cake (still on the cardboard cake round) on a wire rack set in a baking pan. Pour enough ganache glaze over cake to fully coat, shaking pan gently to help spread ganache if necessary. Let sit for 15 to 20 minutes. The ganache in the baking pan may be strained through a fine sieve and added back into glaze. Pour remaining glaze over cake; allow excess to drip off sides. If top is not smooth, gently shake pan, or run an offset spatula quickly over surface. Allow to set at least 30 minutes before serving.