Melt 2 tablespoons of butter and toss with the panko breadcrumbs and a pinch of smoked paprika. Set aside.
Cook your noodles in salted water until they are just al dente. Drain and set aside, but do not rinse—the starch helps the cheese sauce cling to the pasta.
In a large saucepan, melt the remaining 4 tablespoons of butter. Add the minced shallots and cook until translucent. Stir in the garlic and lemon zest, sautéing for just 30 seconds until the kitchen smells like a coastal bistro.
Stir in the flour and cook for 1 minute to remove the raw taste. Gradually whisk in the milk and heavy cream. Add the Old Bay, smoked paprika, and nutmeg. Simmer until the sauce is thick enough to coat the back of a spoon.
Turn off the heat and stir in the Fontina, White Cheddar, and Parmesan. Once the sauce is a velvety gold, gently fold in the shrimp and lump crab meat.
Combine the seafood cheese sauce with the cooked pasta. Transfer to a greased 9x13 baking dish and blanket with the prepared panko topping.
Bake at 350°F for 25–30 minutes. You want the seafood to be heated through and the breadcrumbs to be a deep, toasted gold.