Preheat your oven to 350°F and line several baking sheets with parchment paper.
In a large, heat-safe bowl add the granulated sugar, brown sugar, butter and crème fraîche and set over a medium saucepan of simmering water. Stir frequently until melted and smooth. Take the bowl off of the heat and whisk in the eggs, one at a time not adding the next until the first is completely blended. Continue to whisk the mixture until it’s thick and frothy for about 2 minutes more. Whisk in the milk and vanilla until fully incorporated.
In a medium bowl whisk together the all-purpose flour, bread flour, baking soda and sea salt. Add this to the wet ingredients and fold until the cookie dough is almost blended. You still want to see streaks of flour. With the dough still warm, add the chocolate chunks to the dough and mix until evenly distributed throughout. If you want a marbled effect, give the dough several more folds until you see streaks of melted chocolate. At this point you can either bake the cookies immediately or stash the dough in the fridge until it’s firmed up a bit. If later, press some plastic wrap over the surface of the dough and stash in the fridge. If using immediately, fill a ¼ cup cookie scoop or measuring cup with the dough and plop it on the prepared baking sheet, nudging it into a sphere and allowing about 3 1⁄2 inches of space between the dough to allow for spread. Sprinkle each with a pinch of sea salt flakes, if using.
Bake one sheet at a time in the center of the oven for about 12 minutes. They will look slightly underdone. Allow the cookies to cool on the baking sheet for 10 minutes, and then move to a rack to finish cooling.