Add cubed unsalted butter to a medium saucepan over medium heat. Allow the butter to melt, then continue cooking. Transfer the browned butter to a large mixing bowl before the milk solids burn. Whisk in Tbsp white miso paste until well mixed. Allow the butter mixture to cool slightly.
In a medium bowl, whisk together all-purpose flour, baking powder, baking soda, and Kosher salt.
To the cooled brown butter miso mixture, add brown sugar and granulated sugar, then whisk well to combine. Add large egg and vanilla bean paste, then whisk. The mixture will lighten in color and become very smooth.
Add the dry ingredients all at once, then use a spatula to gently fold into the wet ingredients until only a few streaks of flour remain.
Use a cookie scoop (1-ounce) to measure out cookie dough. Press semi-sweet chocolate into the top of each cookie, then transfer to the prepared baking sheet leaving a couple inches in between each.
Bake until the edges are golden brown. The centers may look slightly underbaked, but this is okay! Sprinkle each cookie immediately with a pinch of flaky sea salt. Cool slightly, then use a spatula to transfer the cookies to a cooling rack. Repeat with remaining cookie dough. Enjoy!