Baked Penne with Squash and Goat Cheese

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Topping:

1/2 cup panko breadcrumbs

2 tablespoons olive oil 

1/4 teaspoon kosher salt 

Pasta:

4 tablespoons (1/4 cup) unsalted butter

2 shallots, chopped 

1/4 teaspoon red pepper flakes 

2 teaspoons kosher salt, plus additional for the pasta water

1/4 cup all-purpose flour 

4 cups whole milk 

8 ounces goat cheese 

1 1/2 cups shredded mozzarella

One 10-ounce delicata squash, halved lengthwise, seeds discarded and sliced into 1/4-inch half-moons 

1 pound penne rigate pasta 

1/2 cup freshly grated Parmesan

1 pound broccoli rabe, trimmed and chopped into 1-inch pieces