How to Make It
Preheat oven to 350°F. Lightly grease a 13 x 9-inch baking dish. Bring a large pot of salted water to a boil. Add pasta and cook until al dente, about 7 minutes (you want the noodles undercooked here since they keep cooking in the oven). Set aside.
Melt butter in a large skillet over medium-low. Add onion and jalapeño; cook, stirring often, until onions are soft and translucent, about 10 minutes. Add flour, Taco Seasoning, and salt; cook, stirring constantly, until darkened, about 3 minutes. Gradually whisk in milk. Increase heat to medium and simmer, whisking constantly, about 4 minutes. Continue cooking, whisking constantly, until thickened, 2 to 4 minutes. Stir in chiles. Add Monterey Jack cheese and 1½ cups of the Cheddar cheese; cook, whisking constantly, until cheese is melted and smooth, about 2 minutes.
Remove mixture from heat and stir in cooked pasta. Spoon mixture into prepared baking dish.
Toss together tortilla chips and remaining ½ cup Cheddar cheese in a bowl. Sprinkle evenly over top of pasta mixture. Bake until bubbling and top is golden brown, 40 to 45 minutes. Let stand 5 minutes; garnish with scallions.