Adjust oven rack to upper-middle position and heat oven to 425 degrees. Season chicken with pepper and arrange skin side down in 12-inch ovensafe skillet. Whisk vinegar, honey, soy sauce, ketchup, granulated garlic, and pepper flakes together in bowl and pour over chicken.
Bake chicken for 20 minutes. Flip chicken skin side up and continue to bake until skin is spotty brown and meat registers 195 to 200 degrees, 20 to 25 minutes longer. Transfer chicken to serving platter. Carefully pour pan juices into fat separator (skillet handle will be hot) and let settle for 5 minutes.
Dissolve cornstarch in water in small bowl. Return defatted juices to skillet and whisk in cornstarch mixture. Bring sauce to boil over high heat and cook until syrupy and spatula leaves trail when dragged through sauce, 7 to 9 minutes. (You should have about 3/4 cup sauce.) Season with pepper to taste.
Off heat, return chicken to skillet and turn to coat with sauce. Flip chicken skin side up and sprinkle with sesame seeds.