Step 1Bring a pot of salted water to a boil for the pasta. Heat the oven to 350 degrees, and butter a 13-by-9-inch baking dish. Cook the pasta, then drain and rinse briefly under cold running water. Set aside.
Step 2Melt 1/4 cup butter in a saucepan over medium heat. Add the minced onion and cook until soft, about 5 minutes. Stir in the flour to make a paste, and cook for 2 minutes to remove the raw flour taste. Add the milk, a bit at a time, stirring constantly, until the mixture thickens.
Step 3Stir in the goat cheese until thoroughly blended. Stir in 4 cups cheddar and cook until melted and smooth. Stir in the green chile, adding more to taste. Season to taste with about 1 teaspoon salt and a generous grinding of black pepper.
Step 4In a small saucepan, melt the remaining 2 tablespoons butter and stir in the panko bread crumbs. Remove from the heat and stir in the reserved cheddar cheese.
Step 5Stir the cooked pasta into the cheese mixture and spoon it into the prepared baking dish, evening the top with the back of the spoon. Sprinkle the bread crumb mixture evenly over the top. Bake until the mixture is beginning to brown and bubble, about 40 minutes.