Preheat oven to 475 degrees. Bring a large pot of salted water to a boil. Meanwhile, line a rimmed baking sheet with parchment paper. Toss tomatoes with oil on prepared baking sheet; season with salt and pepper. Roast until lightly browned and soft, 8 to 10 minutes; set aside.
Cook pasta in boiling water until al dente, according to package instructions. Drain; set aside.
While pasta is cooking, melt butter over low heat in a large saucepan. Add flour; cook, whisking, 1 minute. Gradually, whisk in milk, then nutmeg, 1/2 teaspoon coarse salt, and a pinch of pepper; bring to a simmer. Cook, whisking constantly, until thick enough to coat the back of a spoon, 2 to 3 minutes. Stir in cheese until melted.
Add cooked pasta to cheese mixture; stir to combine. (Sauce will thicken as it stands.) Serve topped with tomatoes and, if desired, additional grated cheddar.