Preheat the oven to 350°F and line a 12-cup muffin pan with paper liners.
In a large bowl, whisk together the warm water, melted chocolate chips, and cocoa powder until smooth and glossy.
Whisk in the eggs, vegetable oil, vanilla bean paste, and white vinegar until the mixture is smooth.
Add the flour, granulated sugar, baking soda, and fine salt to the bowl and whisk just until the batter is combined and no dry streaks remain.
Divide the batter evenly among the 12 liners, filling each about 3/4 full.
Bake for 18 to 20 minutes, until the tops spring back lightly and a toothpick inserted in the center comes out with moist crumbs.
Let the cupcakes cool in the pan for 5 minutes, then transfer to a wire rack to cool completely.
For the frosting, beat the room-temperature butter in a mixing bowl until smooth and creamy.
Add the powdered sugar gradually, mixing on low speed until combined, then increase to medium speed and beat until fluffy.
Add the 1 tbsp heavy whipping cream and 1/4 cup raspberry jam to the frosting and beat until smooth and pink, suitable for piping.
For the ganache, place the 1/2 cup semi-sweet chocolate chips in a heatproof bowl.
Heat the 1/3 cup heavy cream in a small saucepan or microwave until steaming but not boiling, then pour over the chocolate chips.
Let stand for 1 to 2 minutes, then stir until the mixture becomes smooth and glossy; set aside to cool slightly until pourable but not hot.
Once the cupcakes are completely cooled, use a small knife or cupcake corer to remove a small cone of cake from the center of each cupcake.
Fill each cavity with about 1 to 2 teaspoons of the remaining 1 cup raspberry jam, then replace a piece of the removed cake to cover the jam.
Pipe or spread the raspberry frosting on top of each filled cupcake.
Drizzle the slightly cooled ganache over the frosted cupcakes.
Garnish each cupcake with a fresh raspberry if desired, then serve or chill briefly to set the ganache.