Preheat the oven to 350°F. Insert paper liners in a 12-cup cupcake tin and set it aside.
In a medium bowl, sift together the all-purpose flour, pastry flour, baking powder, baking soda, and salt. In a large bowl, whisk together the melted butter, applesauce, and yogurt. Add the sugar and stir to combine. Add the milk. Then add the eggs, one at a time, whisking until each one is incorporated into the batter. Stir in the vanilla extract. Slowly add the dry ingredients to the wet, folding gently until completely combined. Scoop a heaping ¼ cup of the batter into each cupcake liner. Gently tap the tin against the counter several times to remove any air bubbles.
Place the tin in the oven and bake until a toothpick inserted in the center of a cupcake comes out clean, about 25 minutes. Remove the tin from the oven and set it aside to cool for 5 minutes; then transfer the cupcakes to a wire rack to cool completely.
Meanwhile, to make the vanilla bean frosting: Combine the whipping cream and sugar in a medium bowl. On a cutting board, split the vanilla beans in half lengthwise. Then, using the tip of the knife, carefully scrape out the seeds and add them to the cream. Using an electric stand mixer or handheld mixer, whip until stiff peaks form, about 5 minutes.Top each cooled cupcake with 1 tablespoon of the whipped cream frosting and garnish with a raspberry. Serve immediately, or store in an airtight container in the refrigerator for up to 3 days.