Preheat the oven to 350°F (175°C) and line the muffin pan with 12 paper cupcake liners.
In a medium bowl whisk together the flour, cocoa powder, baking powder, baking soda, and salt, then set aside.
In another small bowl combine the finely chopped strawberries, lemon juice, and 1 tablespoon granulated sugar, stirring and letting them macerate while you prepare the batter.
In a large mixing bowl beat the softened butter, granulated sugar, and brown sugar with a mixer on medium speed until light and fluffy, about 2–3 minutes.
Add the eggs one at a time to the butter mixture, beating well after each addition, then mix in the vanilla extract.
Add half of the dry ingredients to the wet mixture and mix on low just until combined.
Pour in the milk and mix on low until mostly incorporated.
Add the remaining dry ingredients and mix just until no dry streaks remain, scraping down the bowl with a spatula as needed.
Gently fold the macerated chopped strawberries and their juices into the batter with a spatula until evenly distributed.
Divide the batter evenly among the 12 cupcake liners, filling each about two-thirds full.
Bake the cupcakes for 18–20 minutes, or until a toothpick inserted in the center comes out with a few moist crumbs.
Remove the pan from the oven and let the cupcakes cool in the pan for 5 minutes.
Transfer the cupcakes to a wire cooling rack and let them cool completely, about 30–40 minutes.
While the cupcakes cool, heat the heavy cream in a small saucepan over medium-low heat until steaming but not boiling.
Place the chocolate chips in a heatproof bowl and pour the hot cream over them, letting it sit for 2–3 minutes.
Add 1 tablespoon butter to the chocolate and cream, then whisk gently until smooth and glossy.
Let the ganache sit at room temperature for 10–15 minutes until it thickens slightly but is still pourable.
Once the cupcakes are completely cool, dip the top of each cupcake into the ganache or spoon the ganache over the tops, letting excess drip off.
If desired, transfer some ganache to a piping bag and pipe a small swirl in the center of each cupcake for extra height.
Press one whole dry strawberry gently onto the center of each cupcake while the ganache is still soft so it adheres.
Let the ganache set at room temperature for about 10 minutes before serving or refrigerating.