Prep the oven and pan. Position a rack in the center of the oven and preheat the oven to 350°F. Lightly spray a 9 x 5-inch loaf pan with cooking spray and line with parchment paper, leaving a 2-inch overhang on the pan's two long sides. Spray the parchment, too.
Make the dry mix. In a medium bowl, whisk together the almond flour, cocoa powder, baking powder, and salt.
Make the wet mix. In a large bowl, mix together the melted butter, sugars, egg, egg yolk, and vanilla until just combined.
Make the batter. Sprinkle the dry mix over the wet mix and stir until just combined.
Assemble the brownies. Pour the batter into the prepared pan and use an offset spatula to smooth the top. Sprinkle the batter with chocolate chips. Bake the brownies. Bake for 33 to 35 minutes, or until a skewer inserted into the center of the brownies comes out with a few crumbs attached. Cool completely on a wire rack before slicing. Serve and store. Run a butter knife or offset spatula along the edges of the pan and use the overhanging parchment as handles to lift the brownies out of the pan and onto a cutting board. Follow the instructions in the baker's notes to slice into 8 petite brownie squares, or 2 large bakery-style brownies. Garnish with flaky salt and serve. The brownies can be stored in an airtight container or zip-top bag at room temperature for up to 3 days.