Position racks in upper and lower thirds of oven and preheat to 350°F. Line two large baking sheets with parchment paper.

In a medium bowl, whisk together flour, baking soda, and fine sea salt until evenly combined.

In a stand mixer fitted with the paddle attachment, beat butter and miso on medium speed until the miso is fully incorporated and no streaks remain, about 1 minute. Add both sugars and beat on medium-high until light and fluffy, 3-4 minutes. Scrape down bowl halfway through.

Beat in whole egg, egg yolk, and vanilla on medium speed until fully combined and mixture looks glossy, about 1 minute. Scrape down bowl and beater.

Add flour mixture all at once and mix on low speed just until a few flour streaks remain. Add chocolate chips and mix on low until evenly distributed and no dry flour remains. Do not overmix.

Using a 1.5-tablespoon cookie scoop or spoon, portion dough into 24 balls. Place 6-8 per sheet with 2 inches between them. Bake until edges are golden brown and centers look slightly underdone, 10-12 minutes, rotating pans and switching racks halfway through.

Immediately sprinkle warm cookies with flaky sea salt. Let cool on pans 5 minutes, then transfer to a wire rack to cool completely. Cookies will firm up as they cool.