In the bowl of a stand mixer fitted with the paddle attachment (or using a hand mixer), cream together butter, brown sugar, sugar, and salt until smooth. Scrape down bowl as needed.
Add egg and egg yolks one at a time mixing on low speed until fully incorporated. Add molasses and mix on medium speed for about 1 minute until batter is thick, fluffy, and smooth.
In a separate bowl, whisk together flour, baking soda, and baking powder. Add to mixing bowl and mix on low speed until combined. Fold in chopped walnuts and chocolate chunks. Cover bowl with plastic wrap and let chill in the fridge for 30 minutes.
Scoop cookie dough into ½ cup mounds using a #8 scoop or a measuring cup. Place on a parchment lined baking sheet. Cover with plastic wrap and place in the freezer for 1 hour, or until solid.*see note for varied cooking times.
Preheat oven to 350° F. Space frozen cookie mounds at least 3 inches apart from each other on a parchment lined baking sheet. (5 mounds will fit on a standard half sized baking sheet.) Bake for 18-20 minutes, until the edges of the cookies are set, but the center is still soft.
From the oven, immediately sprinkle hot cookies with sea salt flakes. Allow cookies to cool on baking sheet. It will take a few minutes for cookies to regain their structure. The warm cookies will be very soft and delicate. Allow cookies to cool before removing from pan.