Blend the cottage cheese with the vanilla in a high speed blender until completely smooth with no curds visible at all. Doing this first will take the chill off before adding it into the dough.
Melt the butter in a light bottomed saucepan over medium high heat, stirring constantly. When the bubbling slows and changes in sound, lower the heat to medium low and keep stirring until the butter smells nutty and turns deep amber, about 5 to 7 minutes total. Pour it into a large mixing bowl and scrape every bit of the toasted milk solids from the bottom of the pan in with it. It should weigh close to 70g now.
Add the brown sugar, honey, and instant coffee to the hot butter, stir briefly to combine, and let the mixture sit for 5 minutes. The coffee needs the hot liquid to dissolve, which is why it goes in here rather than with the dry ingredients.
Whisk for about 1 minute, until the mixture looks like very wet sand and has pulled together. Stop there and do not whip air into it. If using a stand mixer, the paddle attchment is fine for this.
Let the mixture cool to warm before continuing, since hot butter will scramble the yolks.
Whisk the egg yolks into the butter and sugar for about 2 minutes, until creamy and lighter but not fluffy.
Add the blended cottage cheese and whisk until smooth, then add the milk and stir gently just until incorporated.
Whisk the flour, baking soda, and fine sea salt together in a separate bowl, then fold them into the wet mixture by hand with a rubber spatula. Fold in the chocolate chips. If using a stand mixer, go slow here as to not over mix.
Cover the bowl and refrigerate for 8-12 hours. The dough will feel loose when you cover it. Do not add flour, it firms up as the flour hydrates.
Preheat the oven to 350°F and line two half sheet pans with parchment paper.
Portion the cold dough at 80-85g each for 12 cookies. Press each portion into a thick disc rather than leaving it as a ball, spacing them well apart on the pans. Press extra chocolate chunks onto the tops and finish with flaky sea salt.
Bake for 14 minutes, until the edges are golden and set and the centers still look soft and matte. If they seem to be domeing, pull the pan at five minutes a tap the tray onto the counter a few times, then continue to bake.
Cool on the pan for 10 minutes, then transfer to a cooling rack to finish.