Preheat the oven to 350 F and line a 9x9-inch baking pan with parchment paper, leaving an overhang on two sides.
In a large bowl, whisk together the melted butter and brown sugar until smooth. Add the egg, egg yolk, and vanilla extract and whisk until well combined and slightly thickened.
Add the gluten free 1-to-1 baking flour, baking soda, and salt. Stir with a rubber spatula until just combined. Fold in 1 cup of the chocolate chips.
Spread the batter evenly into the prepared pan. Scatter the remaining 1/4 cup chocolate chips over the top and sprinkle lightly with flaky sea salt.
Bake for 22 to 26 minutes until the edges are golden and set but the center still looks slightly underdone. Let cool completely in the pan before lifting out using the parchment and slicing into bars.