Put a baking sheet on the middle oven rack and preheat to 450 degrees F. Bring a large pot of salted water to a boil. Toss the squash with 1 tablespoon olive oil, 1/4 teaspoon salt and pinch of red pepper flakes. Spread on the hot baking sheet and roast, flipping halfway through, until browned and tender, about 30 minutes.
Meanwhile, add the broccoli rabe to the boiling water and cook until bright green and tender, about 2 minutes. Transfer to a colander using a slotted spoon and run under cold water to stop the cooking; pat dry. (Reserve the boiling water.) Pulse 1 cup of the broccoli rabe, the walnuts, garlic, 1/2 teaspoon salt and the remaining 1/2 teaspoon red pepper flakes in a food processor until finely chopped. Add 2 tablespoons water and the remaining 2 tablespoons olive oil and process until thick and smooth. Add 2 tablespoons cheese and pulse to incorporate.
Add the pasta to the boiling water and cook as the label directs for al dente. Reserve 1 cup cooking water, then drain. Return the pasta to the pot and add the remaining cooked broccoli rabe and 1/2 cup of the reserved cooking water. Cook over medium-high heat, stirring, until heated through, about 1 minute. Stir in the pesto, adding more cooking water as needed to loosen; season with salt and pepper. Add the squash and gently toss. Divide among bowls and sprinkle with the remaining 2 tablespoons cheese and more pepper.