Arrange cubed squash on a baking sheet lined with parchment paper. Drizzle two tablespoons of olive oil and mix to coat. Sprinkle salt and pepper over squash and place in the oven for about 15 minutes, or until slightly tender. Once the squash is out of the oven, turn the temperature down to 375°.
In a large skillet add the remaining olive oil and pancetta and cook, stirring frequently until browned.
Once pancetta is nicely browned, and the shallots and sauté until golden. Set aside.
Melt butter in a heavy bottomed pot over medium heat and sprinkle flour over top. Whisk continuously for about three to four minutes, making sure butter and flour is well combined. Slowly whisk in all the milk, and bring to a boil. Reduce the heat to a simmer and continue to whisk for about ten minutes or until thick.
Whisk in nutmeg and remove from heat. Once off the heat, mix in mozzarella, 3/4 cup parmesan and the egg. Mix well to combine, season with salt and pepper and set aside.
Bring a large pot of water to a boil and add one tablespoon of salt. Add rigatoni, stirring occasionally until water returns to a boil. Cook for about eight to ten minutes, or until pasta is al dente. Drain pasta and set aside.
In a large bowl combine pasta, cheese sauce, squash and pancetta shallot mixture. Mix well until combined.
Add half the pasta mixture to a Dutch oven, and dot the top with half the ricotta. Top with remaining pasta and finish with remaining ricotta and parmesan.
Cover in tin foil, bake for 30 minutes and remove from the oven. Turn on the broiler and finish under the broiler for an additional five to seven minutes (uncovered), or until everything is golden and bubbly.