Preheat oven to 425 degrees F. Toss together in a large bowl the carrots, zucchini, garlic, eggplant, red pepper, onion, vegetable broth, thyme, salt and pepper. Spread the mixture in a single layer on a large baking sheet lined with parchment paper or foil.
Roast for about 35 minutes or until golden brown and tender-crisp. Set aside.
Bring a large pot of salted water to a boil.
Make the cheese sauce: Heat the oil in a large saucepan over medium-high heat. Add the flour and cook, stirring, for 1 minute. Slowly whisk in the milk and continue whisking gently until the mixture is thick enough to coat the back of a spoon, about 5 minutes. Add the mustard, cheddar and parmesan cheeses, salt and pepper and whisk until smooth. Remove from the heat.
Meanwhile, cook the macaroni in the boiling water until al dente, about 8 minutes. Drain well and add to the cheese sauce. Add the roasted vegetables and stir to combine.