In small bowl whisk together mustard, honey, 1 teaspoon salt, and ½ teaspoon pepper. Reserve ¼ cup of honey-mustard mixture for basting chicken. Place chicken into gallon-size zipper-lock bag and pour rest of honey-mustard mixture in. Zip bag and shake to coat chicken, and chill for at least 30 minutes or up to 2 hours.
Move oven rack to middle position and preheat to 350 degrees F. Lightly spray 9x13-inch pan (or any other 3 quart baking dish) with nonstick cooking spray. Place chicken in pan and top with onion slices. Cover with foil and bake for 35-40 minutes, or until chicken is no longer pink and juices run clear.
Meanwhile, cook bacon in 10-inch skillet over medium heat until crisp, 5 to 7 minutes. Transfer bacon to paper towel–lined plate.
When chicken is cooked, uncover it, spread with reserved honey-mustard mixture, top with bacon and cheese and broil until cheese is nice and bubbly. Watch the chicken while it’s under the broiler because it can go from beautifully cheesy to burnt very quickly!
Remove chicken from oven, top with chopped tomatoes and green onions, and serve with lime wedges!