Whisk flour, baking soda, and salt in a large bowl and set aside. Melt butter over medium heat in a saucepan. Butter will foam. Be sure to whisk consistently during this process. After a couple of minutes, the butter will brown on the bottom of the pan. Continue to whisk and remove from heat as soon as it's brown throughout and gives off a nutty aroma. Set aside to cool.
Mix the butter and sugars with an electric mixer until blended through. Beat in egg, yolk, vanilla, and yogurt just until combined. Add dry ingredients slowly and beat on low until combined. Gently fold in all chocolate chips.
Chill your dough for 2 hours in the refrigerator. Chill your fillings as well.
Preheat oven to 350. Once dough is chilled, measure 1 to 1 1/2 tbsp dough and roll into ball. Flatten very thinly in your hand. Place 1/2 tsp nutella and 1/2 tsp speculoo in the middle and fold the dough gently around it. Make sure no filling is seeping out. Add more dough if that is the case. Place dough balls on cookie sheet and flatten gently with your hand.
Bake cookies 9-11 minutes or until edges begin to turn golden brown. They'll continue to cook in the middle once they're out of the oven. Cool on sheets at least 2 minutes, then sprinkle with sea salt. Remove from baking sheets after a few minutes and transfer to wire rack to cool completely. Repeat with remaining dough.