In a large bowl, whisk together rye flour, salt, and baking soda. Set aside.
In the bowl of a stand mixer, add 56 grams (4 Tbsp) cold butter, brown sugar, sugar, vanilla, instant coffee granules, cinnamon, and nutmeg. Set aside.
Melt remaining 114 grams (8 Tbsp) butter in a heavy bottomed sauce pot over medium heat. Occasionally swirl pot to ensure even heating. The mixture will bubble and foam as it cooks. The bubbling will be vigorous at first, but will subside and lessen as butter cooks.
Continue to cook until butter smells nutty and the milk solids at the bottom of the pot have turned rich golden brown in color. Remove from heat and pour brown butter (along with browned milk solids) into stand mixer bowl over sugar mixture. Let sit for 5 minutes.
Attach paddle to stand mixer. Beat mixture on medium speed for 2 minutes. Mixture will be dark in color and look broken or oily on the surface.
Add egg and egg yolk. Beat on medium speed for 3 minutes until mixture is creamy in color and has thickened in consistency. Scrape down sides of bowl to ensure even mixing.
Add dry flour mixture. Mix until just combined, and there are no longer any dry streaks of flour. Fold in chocolate chips until evenly distributed.
Transfer dough to a clean bowl. Cover tightly with plastic wrap or lid. Chill in the fridge overnight, at least 6 hours.
Remove dough from fridge and let sit at room temperature for 1 hour to soften. Use a size 24 scoop to portion out the cookie dough. Place scoops on a parchment lined baking sheet. Cover and place in the fridge while oven preheats.
Preheat oven to 350°F. Line several baking sheets with parchment paper or reusable silicone baking mat.
Place chilled cookie portions at least 3-inches apart on prepared baking sheet. Bake for 8 minutes. Rotate baking sheets. Bake for another 6-8 minutes until cookies have spread and are set along the edges.
Immediately sprinkle hot cookies with sea salt flakes, if using. Allow cookies to remain on hot baking sheet for 5-7 minutes before using an offset spatula to transfer warm cookies to wire rack. Cool to room temperature or eat warm!