Make the Miso Marinade: In a bowl, whisk together miso paste, honey, soy sauce, vinegar, garlic, ginger, sesame oil, and water until smooth.
Marinate the Chicken: Season thighs with salt and pepper, coat in the marinade, and let sit 30 minutes (or up to overnight in the fridge).
Bake: Preheat oven to 400°F. Arrange the chicken in a foil-lined baking dish and bake 35-45 minutes, or until internal temp reaches 175-185°F. Broil the top for the last 2-3 minutes for caramelization.
Make the Scallion Rice: Cook rice according to package directions. Sauté the white parts of the scallions in butter, then stir into the cooked rice with the scallion greens and optional sesame oil.
Optional Sticky Miso Glaze: Simmer the miso, honey, soy sauce, vinegar, and water in a pan until thick and glossy. Drizzle over the cooked chicken.
Serve: Plate the scallion rice, top with miso chicken thighs, and drizzle with extra glaze. Garnish with sesame seeds and scallions.