Preheat oven to 375°F (190 °C). Grease a 10" x 7" baking pan.
Cook the pasta: in a large pot of salted water until 2 minutes shy of al dente as per package instructions. Reserve ¾ cup of warm pasta water, then drain it.
Crisp the guanciale: Heat olive oil in a large frying pan over medium heat. Add guanciale and cook 5–7 minutes until golden and crisp. Remove with a slotted spoon and place on a paper towel-lined plate, leaving a thin layer of rendered fat in the pan.
Sauté aromatics: Add the onions to the pan, cook for 2-3 minutes until soft and fragrant. Then stir in the garlic for another minute.
Whisk the sauce: In a medium bowl, mix pumpkin purée, egg yolks, whole egg, Parmesan, salt, and pepper until smooth and glossy.
Combine pasta and sauce: Add the drained pasta to the pan with the onion and garlic. Remove from heat (to prevent scrambling), pour in the sauce and toss quickly. Stir in thyme. Gradually add warm reserved pasta water, one tablespoon at a time (only if needed), while tossing constantly, until the sauce becomes creamy and coats the pasta evenly.
Add crunch: Fold in half the guanciale and half the pistachios.
Assemble the bake: Transfer to the prepared baker. Top with breadcrumbs, remaining guanciale, pistachios, and a few dots of butter.
Bake: for 15–20 minutes, until golden and bubbling. For a crispier top, broil 1–2 minutes (watch closely).
Finish & serve: Place in a shallow bowl with extra parmesan cheese and a final grind of black pepper. Rest 2–3 minutes before serving.