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Arrange a rack in the middle of the oven and heat the oven to 375°F. Coat the wells of a standard 12-well muffin pan with cooking spray.
Cut 14 tablespoons unsalted butter into cubes. Place in a small microwave-safe bowl and microwave until melted, about 1 minute. Drain 1 (20-ounce) can pineapple slices, reserving the juice. Cut the pineapple into roughly 1/4-inch pieces (about 1 1/3 cups).
Place 2/3 cup packed dark brown sugar, 7 tablespoons of the melted butter, 2 tablespoons of the pineapple juice, and 1 teaspoon of the kosher salt in a small bowl and stir until well combined. Spoon 1 tablespoon of the sugar mixture into each muffin well. Spoon 1 1/2 tablespoons of the diced pineapple into each well; pressing down with the back of a spoon to ensure the fruit is tightly packed.
Bake until sugar bubbles around the fruit, darkens in color slightly, and the pineapple begins to becomes translucent, 15 to 20 minutes. Remove from the oven and set aside to cool while you make the cake batter.
Line a rimmed baking sheet with parchment paper or aluminum foil.
Place 2 1/2 cups sifted cake flour and 2 teaspoons baking powder in a medium bowl and whisk until well combined.
Place the remaining 7 tablespoons melted butter, remaining 1 teaspoon kosher salt, 1 cup granulated sugar, 2 large eggs, and 1 tablespoon vegetable oil in in a large bowl and whisk until creamy and well combined. Finely grate the zest of 1 large lemon into the bowl. Add 1 cup sour cream, 1/3 cup of the pineapple juice, 1 teaspoon vanilla bean paste, and 1/4 teaspoon grated nutmeg, and whisk until well combined.
Add flour mixture to butter mixture and mix with a whisk just until it comes together and no large, dry streaks of flour remain. Switch to a rubber spatula and fold the batter a few times, scraping the sides and bottom of the bowl to ensure everything is well mixed. Using a 2-ounce cookie or ice cream scoop, scoop the batter into each muffin well to fill about 3/4 full. (If you have any leftover batter, you can bake off a few extra plain cupcakes or discard.)
Place the muffin pan on the baking sheet. Bake until the cupcakes springs back when lightly pressed in the middle and a cake tester inserted in the center of one comes out clean, 18 to 22 minutes.
Let the cupcakes cool in the pan for 10 minutes. Gently run a small offset spatula or butter knife around the edge of each cupcake to loosen. Remove the parchment or foil from the baking sheet. Invert the baking sheet over the muffin pan. Grasping the muffin pan and baking at the same time with kitchen towels or oven mitts to protect your hands, flip them over in one motion. Carefully lift the muffin pan away; if any pineapple remains stuck, just spoon it back onto the cupcake. Let the cupcakes cool for at least 15 minutes more before serving with whipped cream or ice cream and a cherry on top if desired.