For the homemade toffee bits: Line a large baking sheet with parchment paper or silicone baking mats.
In a heavy-bottomed saucepan over medium heat, melt the butter. Once partially melted, add the brown sugar and salt and whisk until smooth.
Continue cooking over medium heat, stirring constantly, until the mixture is smooth, thickened and deep golden brown, about 8-10 minutes and the mixture measures 300°F.
Remove from the heat and immediately pour onto the prepared baking sheet. Using a spatula, spread into an even layer.
Let cool until hardened, about 20 minutes. Break into small pieces.
You’ll only use about a cup of toffee for this recipe. Store the rest in an airtight container for up to 2 weeks.
For the cookie dough: Melt the butter in a medium skillet over medium-low heat, stirring occasionally.
Once the butter is melted and begins to foam, stir continuously to prevent the milk solids from sticking to the skillet. The butter will change from yellow to golden brown quickly and will have a nutty aroma. Remove from the heat and immediately pour into a medium bowl.
Place the browned butter in the freezer for 10 minutes (or leave at room temperature for 30 minutes) to cool slightly.
Add the brown sugar and granulated sugar to the brown butter. Whisk to combine.
Whisk in the eggs and egg yolk until smooth and creamy.
Add the milk, vanilla, baking soda, baking powder, salt and espresso powder. Whisk until smooth.
Using a rubber spatula, mix in the gluten-free flour and almond flour until almost combined. Stir in the semisweet chocolate and toffee bits and mix just until no dry streaks of flour remain.
Scoop the cookie dough into round balls, about 2 tablespoons per ball. Place the dough balls onto a large plate or a parchment paper-lined large baking sheet. Cover with plastic wrap.
Freeze the dough balls for at least 2 hours or up to 3 months. Transfer to an airtight container if freezing for more than a few hours.
Preheat the oven to 350°F. Line large baking sheets with parchment paper or silicone baking mats.
Place the 6 frozen dough balls on a prepared baking sheet, leaving room for the cookies to spread. Bake for 12-14 minutes, until the cookies have spread and are golden brown (note that these are supposed to be thin and crisp cookies!).
Remove from the oven and top with more pieces of toffee and chopped chocolate if desired. Cool on the baking sheet for 10 minutes. Sprinkle with flaky salt and transfer to a wire rack to cool completely.