Preheat the oven to 350°F (180°C) and line a 9"x13" (23x33cm) pan with parchment paper.
Make the pretzel crust: Stir together all ingredients. Press into the pan.
Make the cookie dough: Add the flour, baking soda, salt, and cornstarch to medium mixing bowl and whisk until combined.
Add the butter, brown sugar, and sugar to a large mixing bowl or bowl of a stand mixer fitted with the paddle attachment. Beat until light and fluffy, about two minutes. Add the milk and vanilla and beat again until creamy.
Add the dry mixture to the wet and mix until just combined.
Fold in 1 cup (140 g) of chocolate chunks.
Gently press the cookie dough evenly on top of the crust.
Top with the remaining 3/4 cup (105 g) chocolate chunks and gently press in. Top with flaky sea salt.
Bake in the preheated oven for 16-18 minutes, until lightly golden-brown. Top with extra sea salt.
Allow to cool and slice into 24 bars.