Preheat oven to 350°F (175°C). Line an 8-inch square metal baking pan with parchment paper, leaving an overhang on two sides for easy lifting. Lightly grease any exposed sides of the pan.

Place the semi-sweet chocolate and unsalted butter in a medium microwave-safe bowl. Microwave in 20–30 second bursts, stirring after each, until completely melted, smooth, and glossy. Let cool for 3–5 minutes until warm but not hot. Alternatively, melt together in a small saucepan over low heat, stirring constantly.

Add the granulated sugar and light brown sugar to the warm chocolate mixture. Whisk until thick and well combined. The mixture may look slightly grainy; this is fine.

Whisk in the 2 large eggs, the extra egg yolk, and vanilla extract. Continue whisking for 30–45 seconds, until the batter thickens slightly and looks shiny. This helps create a chewy texture and shiny, crackly top.

In a separate small bowl, whisk together the gluten free all-purpose flour blend, cocoa powder, baking powder, and fine sea salt until evenly combined and any cocoa lumps are broken up.

Sprinkle the dry mixture over the chocolate mixture. Using a spatula, gently fold until just combined, scraping the sides and bottom of the bowl to incorporate any dry pockets. The batter will be thick; avoid overmixing to keep the brownies tender and fudgy.

If using, fold in the chopped walnuts or pecans and/or a portion of the extra chocolate chips until evenly distributed.

Scrape the batter into the prepared pan and spread it into an even layer with a spatula. If desired, sprinkle the remaining chocolate chips and a pinch of flaky sea salt over the top.

Bake at 350°F (175°C) for 22–28 minutes, depending on your oven and desired fudginess. Begin checking at 22 minutes. A toothpick inserted about 2 inches from the edge should come out mostly clean with a few moist crumbs, while the center may still look slightly soft. The brownies will continue to set as they cool.

Place the pan on a wire rack and let the brownies cool completely, at least 60–90 minutes. Use the parchment overhang to lift the cooled brownies from the pan. Cut into 9 large or 16 smaller squares with a sharp knife, wiping the blade between cuts for clean edges. For extra neat slices, chill the brownies for 30 minutes before cutting.