Preheat your oven to 350°F (175°C). Grease a 9x5 inch loaf pan and line it with parchment paper, leaving an overhang on the long sides.
In a medium bowl, whisk together the gluten free baking flour, almond flour, baking powder, baking soda, and salt. Set aside.
In a large bowl, whisk the melted butter with the granulated sugar and dark brown sugar until smooth and slightly thickened. Add the eggs one at a time, whisking well after each. Stir in the vanilla extract and milk.
Fold the dry ingredients into the wet ingredients using a spatula until just combined. The batter should look thick and almost like cookie dough that has been loosened slightly. Fold in about three-quarters of the chopped chocolate, reserving the rest for the top.
Pour the batter into the prepared pan and spread it evenly. Press the remaining chocolate chunks into the top of the batter, then sprinkle lightly with flaky sea salt.
Bake for 50 to 58 minutes, until the top is set and golden and a toothpick inserted in the center comes out with a few moist crumbs. The center should have just a slight jiggle when you gently tap the pan.
Let the bread cool in the pan for at least 20 minutes. Lift it out using the parchment paper and let it cool on a wire rack for another 15 minutes before slicing. The inside will be dense, gooey, and fudgy like a giant cookie.