Heat a large pot over medium heat. Add n'duja and break into small chunks using a wooden spoon. Continue to heat n'duja until it starts to sizzle and breakdown. Remove 1 tablespoon and set aside. Turn off the flame and set aside pot while you make the breadcrumbs.
Melt 2 tablespoons butter in a medium pan over medium heat. Continue to heat butter until it browns and smells nutty. Add sage and heat for 30 seconds, stirring constantly. Add panko and stir to coat breadcrumbs in butter. Heat until breadcrumbs turn golden brown. Remove from heat and stir in reserved 1 tablespoon n'duja. Set aside.
Return to the other pot and turn back flames to medium heat. Add flour to pot with n'duja and stir to combine. Pour milk and butternut squash puree and stir to combine. Bring to a low simmer and continue to heat until the milk starts to thicken, about 3-4 minutes.
Add sharp cheddar and gruyere, stirring until cheese is melted. Season sauce with salt and pepper and keep warm on low heat.
Meanwhile, cook pasta until al dente. Drain and add to cheese sauce, stirring to coat pasta. Serve mac and cheese into bowls and top with brown butter n'duja breadcrumbs.
Notes
You can prepare the breadcrumbs up to 5 days in advance.