Prepare the Brownies:
Preheat your oven to 350°F (175°C). Line a 9×9 square baking pan with foil or parchment paper, leaving a couple of inches of overhang on two sides for easy removal. Lightly grease the foil or parchment.
In a large mixing bowl, whisk together the melted butter and granulated sugar vigorously for one minute. Add the eggs, water, and vanilla extract, then whisk again for about 30 seconds until combined. Tap off the excess batter from the whisk and set it aside.
Sprinkle the cocoa powder, powdered sugar, flour, and salt over the wet ingredients. Using a rubber or silicone spatula, stir the mixture until it becomes glossy and well combined. Fold in the chocolate chips.
Pour the brownie batter into the prepared pan and smooth the top. Bake for 18-20 minutes, or until a toothpick inserted into the center comes out with moist, fudgy crumbs (but no raw batter). Be careful not to over-bake. Remove the brownies from the oven and let them cool completely on a wire rack before adding the topping.
Make the Topping:
In a medium saucepan, combine the evaporated milk, brown sugar, egg yolks, butter, and salt over medium-low heat. Slowly bring the mixture to a gentle simmer, whisking constantly to ensure even cooking. Once simmering, continue whisking for about 3-4 minutes, until the sugar has dissolved and the mixture has thickened slightly.
Remove the saucepan from heat and stir in the vanilla extract, chopped pecans, and shredded coconut. Spoon the topping onto the cooled brownies and spread it into an even layer. Sprinkle with flaky sea salt if desired.
Allow the topping to firm up before cutting the brownies into squares. You can speed up this process by placing the brownies in the refrigerator. Serve at room temperature for the best flavor.