Preheat oven to 400°F.
Add butternut squash, Brussels sprouts, apple, and 2 tablespoons olive oil to a large mixing bowl. Toss until evenly coated. Add sage leaves and ½ teaspoon salt and toss again. Then, set aside.
In a separate mixing bowl, add remaining olive oil and salt, mustard, garlic, and black pepper. Stir until combined and then add pork chops and rub each chop until evenly coated.
Place chops on a lined baking sheet and lay thyme sprigs over the top. Pour vegetable mixture around chops in a single, evenly spaced layer. Bake for 25 minutes on the middle rack or until pork chop reaches 145°F at center.