Preheat oven to 400°F. Spread the cubed pumpkin out onto a foil-wrapped baking sheet, and toss with olive oil, salt, pepper, and nutmeg. Roast for 20 minutes, toss, and then roast another 20 minutes. Remove from the oven and let cool to room temperature.
As the pumpkin is roasting, prepare the pasta al dente (be careful not to overcook). Drain when finished but do not rinse. Sauté the bacon in a large frying pan and then remove and wrap in paper towels to absorb excess grease. Wipe down the pan and use it to make a roux for the pumpkin sauce – it doesn’t need to be spotless, you just want to remove any bits that might burn.
Brown the butter in the pan by swirling it around over medium heat. You’ll know it’s ready once the butter foams up a bit and then subsides, taking on a subtle nutty aroma. Before it starts to burn, whisk in the flour and let it cook for a minute or two. Slowly whisk the milk into the butter-flour mixture to make the roux, then add the Mascarpone cheese, chopped sage, red pepper flakes, and chicken stock and stir to combine. Mix in the roasted pumpkin. If it’s still a little chunky, smash it up with a potato masher or the back of a wooden spoon until it’s smooth. Turn the heat to low, and mix in half of each of the Gruyere and Parmesan. Remove from heat.
Pour the drained and cooked pasta into an oven-to-table serving dish. Fold in the pumpkin sauce and crumbled bacon. Sprinkle the top with the remaining cheese, and top with the large sage leaves for decoration. Bake for 20-30 minutes.