Position a rack in the upper third of the oven and preheat to 450 degrees F. Bring a medium saucepan of salted water to a boil. Add the macaroni and cook as the label directs; drain.
Mist a baking sheet with cooking spray and arrange the tomato and baguette slices on it in a single layer; season with salt and pepper. Bake until the bread is golden brown, about 7 minutes.
Mince the shallots, carrot and celery in a food processor. Mist a saucepan with cooking spray. Add the vegetables and cook over medium-high heat until softened, 4 to 5 minutes. Add the flour and cook, stirring, 2 minutes. Gradually stir in the broth and bring to a boil; cook, stirring, until thickened, 6 to 7 minutes. Remove from the heat.
Add the milk, cheeses and macaroni and stir until the cheeses melt. Season with pepper. Top the toasts with tomatoes; serve on the soup.