To make the buttermilk, combine milk and lemon juice in a small bowl. Leave out at room temperature until the acid makes the milk start to curdle, at least 10 minutes. (This can be made ahead of time and refrigerated for up to three days.)
Adjust oven racks to the upper-middle and lower-middle positions and preheat oven to 350 degrees. Line three 8-inch round cake pans with parchment paper, coat with nonstick spray, and dust with cocoa powder.
In a large bowl, whisk together flour, cocoa, baking soda, baking powder, and salt until combined.
In a separate bowl, combine the sugar, oil, chocolate, eggs, buttermilk (as prepared above), and vanilla extract and mix well. Add the wet ingredients to the dry ingredients and mix to combine. Stir in boiling water (batter will be very thin). Pour batter into prepared pans.
Bake until a toothpick inserted into the center comes out clean with a few crumbs attached, about 20 to 30 minutes, rotating and switching pans halfway through baking time.
Cool cakes in pan 10 minutes. Run a small knife around the edge of the cakes and flip out on to wire racks. Peel off parchment paper, flip cakes right-side up, and cool completely, at least 2 hours.