Roast the poblano chilies under the broiler until blackened, about 5 minutes per side.
Place the chiles in a paper sack or plastic food-storage bag, close it tightly, and let the for 20 minutes.
Take the chiles out of the bag and rub off the skin.
Remove the stem and seeds and chop the chiles into 1-inch long pieces.
Bring a large pot of salted water to a boil and add the pasta. Cook according to your package's directions and then drain the pasta. You want the pasta to be cooked al dente but not mushy.
Preheat the oven to 375 degrees F.
Grease a large baking dish or a large 12-inch cast-iron skillet, and pour the drained pasta into the dish.
In a pot on low heat melt the butter.
Add the garlic and cook for 1 minute.
Whisk in the flour and cook until a light brown, toasty paste is formed about 1 minute.
Whisk in the milk and stir until it's thickened but still fluid, about 1 to 2 minutes.
Remove the pot from the heat and stir in the mustard powder, cayenne, cumin, lime zest, cilantro, and chopped poblano chiles.
Adjust seasonings and add salt and black pepper.
Slowly add half of the cheddar cheese and stir until it's melted and well combined with the sauce. If the sauce has cooled too much and the cheese won't melt, return the pot to low heat on the stove seems a little thick return it to the stove until soft again. If however, the sauce gets too thick, like a custard, you can thin it by stirring in milk, a teaspoon at a time.
Pour sauce over pasta, top with the remaining half of the cheddar cheese, and bake uncovered for 20 minutes or until brown and bubbling. Sprinkle with Cotija cheese, and serve immediately.