Coat large skillet with cooking spray and heat over medium. Sauté onions and bell pepper about 3 minutes. Add squash and cook, stirring often, about 4 minutes more.
Transfer vegetables to 9" x 13" x 2" roasting pan.
In small bowl, mix thyme, salt, and pepper. Sprinkle over vegetables in roasting pan.
Place chicken halves over squash mixture making sure to cover them.
In small bowl, whisk mustard and applesauce. Apply to chicken with pastry brush. Place chicken in oven and bake until thoroughly cooked, about 1 hour. or until meat thermometer placed in in thigh registers at 180°F.