Preheat the oven to 400°F. Butter a large cast-iron skillet, casserole pan, or a 9 × 13-inch baking dish, and set it aside.
Bring a large pot of salted water to a boil. Add the pasta and cook, following the package directions, until 3 minutes shy of al dente. The pasta should still have a bite to it. Drain, and shake out all the water.
Meanwhile, In a large pot or Dutch oven, melt the butter. Saute the scallions and jalapenos over medium-high heat until soft, about 5 minutes. Whisk in the flour and cook until it is fully incorporated, 1 minute. Add the warm milk and whisk gently over medium heat until the mixture has bubbled and thickened enough to coat the back of a spoon, about 10 minutes. Stir in the salt, pepper, mustard, and most of the grated cheese, reserving 1/2 cup. Add the pasta and toss to combine.
Distribute the mixture evenly in the prepared skillet or baking dish, and sprinkle the remaining cheese over the top. Bake for 20 to 25 minutes, until bubbling and browned. If the top is not browned and toasty, stick the pan under the broiler for 1 minute. Serve piping hot.