Preheat oven to 350 degrees F (175 degrees C). Butter a baking dish.
Bring a large pot of lightly salted water to a boil; add penne and cook, stirring occasionally, until tender yet firm to the bite, about 11 minutes. Drain and transfer to a bowl.
Heat butter in a skillet over medium heat. Whisk flour into melted butter until a thick paste (roux) forms, about 2 minutes. Add nutmeg; cook and stir until incorporated, about 1 minute. Gradually pour beer and milk into roux, whisking constantly until smooth; bring to a boil. Reduce heat to medium low and simmer sauce for 5 minutes; season with salt and pepper.
Remove skillet from heat; stir 2/3 of the Cheddar cheese and 2/3 of the Gruyere cheese into the sauce until melted. Pour sauce over pasta and stir to coat; spoon into the prepared baking dish. Sprinkle remaining Cheddar cheese and Gruyere cheese over pasta mixture; top with bread crumbs.
Bake in the preheated oven until bubbling and cheese is melted, about 40 minutes.