Whisk the all-purpose flour and baking soda in a small bowl to combine; set aside. Toast the macadamia nuts in a dry small skillet over medium-low heat, stirring often, until golden, about 5 minutes. Transfer to a cutting board; let cool. Very coarsely chop (you want to keep the pieces large).
Heat the unsalted butter in same skillet until it foams, then browns, about 4 minutes. Scrape into a large bowl; let cool 1 minute. Add dark brown sugar, granulated sugar, white miso, salt to brown butter and whisk, until sugars are dissolved. Whisk in the egg, room temperature, and vanilla extract. Working in 2 or 3 batches, sift reserved dry ingredients into bowl, folding after each addition until no dry spots remain. Add nuts, semisweet chocolate chips, and white chocolate chips and fold until just combined. Cover and chill dough at least 30 minutes and up to 1 day.
Preheat oven to 350°. Using a #20 cookie scoop (or about 3 Tbsp.), portion out dough, placing 5–6 cookies each on 2 parchment-lined rimmed baking sheets, spacing about 2” apart, and sprinkle with flaky sea salt. Bake cookies, rotating baking sheets front to back and top to bottom halfway through, until golden around edges, 14–16 minutes. Remove from oven and let cookies cool on baking sheets 5–10 minutes, then transfer to wire racks and let cool completely.