To make the croutons, melt the butter in a skillet over medium heat. Add the bread cubes and toast until light golden, 4 to 6 minutes. Transfer to a paper towel-lined plate and season with a pinch of salt. Set aside.
To prepare the pasta, butter the bottom and sides of a 9 x 13-inch casserole dish. Preheat the oven to 350 degrees F. In a medium bowl, toss together the Cheddar, Colby, and Jack cheeses. Put the cooked pasta in a large bowl and add two-thirds of the blended cheese. Set aside.
To make the custard, in a large bowl, whisking between additions, mix together the flour, salt, black pepper, cayenne pepper, mustard, nutmeg, sour cream, egg, onion, heavy cream, and half-and-half. Pour the custard over the pasta mixture and toss to combine.
Pour the macaroni mixture into the prepared baking dish. Cover with the remaining cheese blend. Bake uncovered until the cheese is almost set and the top is just beginning to brown, about 35 minutes. Remove from the oven and sprinkle the croutons over the top. Return the dish to the oven and bake until golden brown, about 10 minutes more.