Heat oven to 375°F. Butter a 3-quart casserole dish; set aside
Place bread crumbs (2 cups), crumbled bacon (8 slices), 1/4 cup Parmesan cheese, and thyme leaves (1/2 teaspoon) in a medium bowl; In a small dish melt 2 tablespoons butter in the microwave. Pour the melted butter into the bowl with the breadcrumb mixture, and toss to combine; set breadcrumbs aside.
In a medium saucepan set over medium heat, heat milk (5 1/2 cups). Melt the remaining 6 tablespoons of butter in a high-sided skillet over medium heat. When butter bubbles, add flour (1/2 cup). Cook, whisking constantly for 1 minute.
While whisking, slowly pour in hot milk. Continue cooking, whisking constantly, until the mixture bubbles and becomes thick.
Remove the pan from heat. Stir in dijon mustard (1 tablespoon), salt (2 teaspoons), nutmeg (1/8 teaspoon), black pepper (1/4 teaspoon), cayenne pepper (1/4 teaspoon), cream cheese (4 ounces), 3 cups smoked Gouda cheese, 1/4 cup Parmesan cheese; set cheese sauce aside.
Fill a large saucepan with water; bring to a boil. Add pasta (1 pound); cook 2 to 3 minutes less than the manufacturer's directions, until the outside of the pasta is cooked and the inside is slightly underdone. (Different brands of pasta cook at different rates; be sure to read the instructions.) Drain pasta well, return it to the pot it cooked in, then pour reserved cheese sauce over the pasta and mix well.
Pour the mixture into the prepared baking dish. Sprinkle the remaining 1 cup smoked gouda cheese and breadcrumbs over top. Bake until browned on top, about 30 minutes. Transfer dish to a wire rack to cool for 5 minutes; serve hot.