Preheat oven to 350°F. Line 12 (1/2-cup) muffin cups with paper liners; coat the liners with cooking spray.
Puree 2 cups raspberries and 1 tablespoon granulated sugar in a blender or food processor until smooth. Strain through a fine-mesh sieve into a small bowl, pressing with a rubber spatula to extract all the puree; discard seeds. Reserve 4 teaspoons of the puree for the frosting.
Whisk whole-wheat flour, cake flour, baking powder, baking soda and salt in a medium bowl. Beat 3/4 cup granulated sugar and oil in a large mixing bowl with an electric mixer on medium speed until combined. Beat in eggs, vanilla and 1 teaspoon lemon zest until well combined. With the mixer on low, alternately mix in the dry ingredients and buttermilk, starting and ending with dry ingredients and scraping the sides of the bowl as needed, until just combined.
Fill the prepared cups half full of batter. Place a scant tablespoon of raspberry puree on each cup (you may have some left over). Divide the remaining batter evenly among the cups. Use a wooden skewer or toothpick to swirl and fold the puree into the batter.
Bake the cupcakes until a toothpick inserted into the center comes out clean, 22 to 24 minutes. Transfer to a wire rack and let cool completely.
Meanwhile, beat cream cheese, confectioners? sugar, 1/2 teaspoon lemon zest and the reserved 4 teaspoons raspberry puree with an electric mixer until smooth. Refrigerate the frosting until very cold, at least 2 hours. Spread the frosting on the cooled cupcakes and decorate with a raspberry on top, if desired.