Wash beets and place in a small roasting pan with 1/2 cup water. Cover and bake for 45 minutes to 1 hour, or until easily pierced with a fork. Dunk the beets in cool water, then using your fingers, slip off the peels. Coarsely chop, then transfer to a blender or food processor and puree. Measure out 2 cups and set aside.
Reduce the oven temperature to 375 degrees F. Lightly coat a 10-cup Bundt or tube pan with oil and dust with flour. In a large bowl, sift together the all-purpose flour, whole-wheat pastry flour, baking soda, and salt. Set aside.
In a double boiler or a small pan over low heat, add the chocolate and 1/4 cup of the oil. Heat just until the chocolate melts. Remove from the heat and stir until well combined. Set aside.
In a large mixing bowl, beat together the eggs and sugar until fluffy. Slowly add the remaining 1/4 cup oil, Greek yogurt, vanilla extract, the chocolate mixture, and the 2 cups beet puree.
Gently add the flour mixture, stirring by hand just until combined.
Pour the batter into the prepared pan.
Bake for 45 minutes, or until a toothpick inserted near the center comes out clean. Transfer the pan to a wire rack to cool for 30 minutes. Run a thin knife along the outer and inner edges of the pan and carefully invert the cake onto the wire rack. Let it cool completely before glazing.
For the glaze: Beat together the cream cheese and powdered sugar until smooth and light. Beat in the milk and vanilla extract. If desired, add a bit more milk or powdered sugar as needed to reach your desired glaze consistency. Drizzle over the cake, letting it run over the top and sides.
Notes
*SERVING SIZE NOTE: In order to make a cake sized for two, I halved the recipe and baked it for 30 minutes in a 5-cup Bundt pan.
TO STORE: Cover and refrigerate leftover cake for up to 4 days.
TO FREEZE: Wrap the cake tightly with plastic wrap and freeze in an airtight, freezer-safe storage container for up to 3 months. Let thaw overnight in the refrigerator before reheating.