Preheat the oven to 450 degrees F. Bring a large pot of salted water to a boil.
Toss the butternut squash with 2 tablespoons of the oil and 1/4 teaspoon each salt and pepper. Bake, stirring once or twice, until golden brown and tender, 12 to 15 minutes.
Heat 2 tablespoons oil in a medium saucepan over medium heat. Add the garlic and red pepper flakes and cook, stirring, until the garlic is golden, about 2 minutes. Add both cans of tomatoes and 1 cup water. Increase the heat to medium-high and bring to a simmer. Reduce the heat slightly, add the basil and simmer rapidly, uncovered, until thickened, 15 to 20 minutes. Discard the basil and season with salt and pepper.
Meanwhile, heat the remaining 1 tablespoon oil in a medium skillet over medium heat. Add the pancetta and cook, stirring occasionally, until browned and crispy, about 8 minutes. Transfer to a large bowl using a slotted spoon.
Cook the penne in the salted boiling water until very al dente, about 2 minutes less than the package directions. Drain the pasta and add it to the bowl with the pancetta.
Add the tomato sauce, butternut squash, half of the Asiago and half of the Parmesan to the bowl and stir well to combine. Transfer the pasta to a 3- to 4-quart baking dish and top with the remaining Asiago and Parmesan. Bake, uncovered, until browned, about 15 minutes. Let the pasta stand about 10 minutes before serving. Tear fresh basil and sprinkle it over the top.
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