Melt the butter in a small saucepan over medium heat, stirring often, until it foams and the milk solids turn golden brown and smell nutty, then transfer to a heatproof bowl and set it over a folded towel in the freezer to cool until thickened but not solid.
While the butter cools, whisk together the all-purpose flour, bread flour, baking soda, and kosher salt in a medium mixing bowl.
Once the butter is ready, beat it in a stand mixer with the brown sugar, white sugar, eggs, and vanilla for about two minutes until light and creamy.
Add the dry ingredients and mix on low speed until the flour is about 75% combined, then toss in the chocolate chunks and chips and mix just until everything comes together.
Press plastic wrap directly onto the dough, cover the bowl, and refrigerate for at least 24 hours and up to 3 days.
When you're ready to bake, let the dough sit at room temperature for about an hour, then scoop it into 140-gram balls and press the tops lightly into a bowl of flaky sea salt.
Chill the salted dough balls while you preheat the oven to 350°F, then line two sheet trays with parchment and place three cookies on each tray, spaced a few inches apart.
Bake for 8 minutes, rotate and switch the trays, then bake another 6 minutes before banging each tray on the counter a few times to help the cookies spread.
Bake 2 to 3 more minutes until the edges are golden and the tops are just set, then bang the trays again to create ripples.
Let the cookies cool on the trays for 5 minutes, then move them to a wire rack and repeat until all the dough is baked.