Preheat the oven to 400 degrees F. Bring a large pot of salted water to a boil. Add the pasta to the boiling water and cook according to package directions. Drain and set aside.
Heat the butter in a medium saucepan over medium-high heat. Add the onion, 2 1/2 teaspoons salt and a few grinds of pepper and cook, stirring occasionally, until golden, about 6 minutes. Add the flour and stir until absorbed. Whisk in the milk and bring to a simmer. Add the spinach and artichoke hearts and simmer until the sauce thickens, about 10 minutes. Stir in the mozzarella and remove from the heat. Add the cooked pasta and stir to combine. Adjust seasoning with salt and pepper. Transfer to a 3- to 4- quart baking dish.
Toss the panko with the oil and sprinkle over the pasta. Bake until the filling is bubbling and the panko is golden, about 40 minutes.
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