Preheat the oven to 350°F. Line a 9×13-inch baking pan with parchment paper and lightly spray with nonstick cooking spray.
Whisk the melted butter and granulated sugar together in a large mixing bowl until smooth.
Add the eggs one at a time, whisking after each addition. Stir in the vanilla extract.
Add the cocoa powder, flour, and salt. Fold together with a rubber spatula just until no dry streaks remain.
Fold in one cup of semi-sweet chocolate chips.
Spread the brownie batter evenly in the prepared pan.
Bake for 28 to 32 minutes, until the edges are set and a toothpick inserted near the center comes out with a few moist crumbs.
Cool the brownies completely in the pan.
Beat the softened cream cheese and four tablespoons of softened butter until smooth and creamy.
Gradually add the powdered sugar and mix until combined.
Add the coconut cream and coconut extract. Beat until smooth.
Fold in the sweetened shredded coconut.
Spread the coconut filling evenly over the cooled brownies. Refrigerate for 30 minutes.
Place 1¼ cups of semi-sweet chocolate chips in a heat-safe bowl.
Heat the heavy cream and one tablespoon of butter over medium-low heat until hot and just beginning to bubble around the edges.
Pour the hot cream over the chocolate chips. Let stand for two to three minutes.
Stir until the ganache is completely smooth.
Spread the ganache evenly over the chilled coconut layer.
Refrigerate for at least one hour, or until completely set.
Lift the brownies from the pan using the parchment paper. Cut into 24 squares with a sharp knife and serve.