Heat 1 tablespoon butter in a medium skillet over medium-high heat. Add the shallots and saute until translucent, about 5 minutes. Mix in the breadcrumbs until coated, then the chile powder and thyme; season with salt. Remove from the heat and set aside.
Preheat the oven to 350 degrees F. Rub 1 tablespoon butter in a 9-by-13-inch baking dish.
Bring a large pot of salted water to a boil. Add the macaroni and cook as the label directs, until tender but still firm to the bite. Drain and set aside.
Meanwhile, melt the remaining 4 tablespoons butter in a large heavy pot over medium-high heat. Add the flour and stir for 1 minute; do not brown. Add the milk in a slow, steady stream, whisking until smooth. Bring to a simmer, then reduce the heat to low and cook, whisking, until the sauce thickens, about 10 minutes. Whisk in 1 cup each mozzarella, cheddar and manchego. Season generously with salt and pepper. Stir in the pasta and remove from the heat. Pour the pasta mixture into the prepared baking dish.
Mix the remaining 1 cup each mozzarella, cheddar and manchego in a medium bowl. Sprinkle over the pasta. Top with the breadcrumb mixture. Cover with foil and bake for 30 minutes. Uncover and bake until the top is golden, about 12 more minutes. Serve immediately.