Preheat oven to 375 degrees F. In a large pot of salted water, cook pasta until al dente, 5–7 minutes. Drain and toss with 2 tablespoons butter. Set aside.

In a large saucepan, add milk, garlic, thyme, bay leaf, onion with clove, and mustard. Warm over medium-low heat until milk starts to steam, about 10 minutes. Remove from heat, set aside, and let the flavors infuse.

To a medium skillet over medium heat, cook bacon until crispy. Remove with a slotted spoon and drain on a paper towel-lined plate. Sauté jalapeño and bell pepper until soft. Remove and transfer to another paper towel-lined plate.

Strain the milk, discarding the solids. To a 10-inch ovenproof skillet over medium heat, add remaining butter and flour. Whisk for 3–4 minutes. Do not let brown.

Whisk the milk into the roux to avoid lumps. Continue to cook, whisking constantly, until thickened, 3–4 minutes. Remove from heat and season with salt, white pepper, and nutmeg. Add the cheddar and Gouda and stir until melted then add the cooked pasta, peppers, half of the bacon, and half of the basil, stirring to thoroughly combine. You can bake this in the skillet, or transfer mixture to a casserole dish.

In a small bowl, combine Parmesan, breadcrumbs, and remaining basil and sprinkle over the top along with remaining bacon. Bake for 25–30 minutes until golden brown and bubbly. Let rest 15 minutes before serving.