Sauté the aromatics: Melt unsalted non dairy butter in a pan and lightly sauté finely chopped garlic cloves, black pepper, nutmeg and red pepper flakes until fragrant. Remove from heat and set aside.
Cook the pasta: In a pot, add water and bring to a simmer. Add pasta and cook, stirring often, until two-thirds of the water is absorbed and the pasta is very al dente (about 5 minutes). Reserve some of the pasta water and then drain the pasta.
Blend the sauce: In a blender, combine; silken tofu, pumpkin purée, nutritional yeast, and a pinch of salt. Blend until smooth, gradually adding some of the reserved pasta water to achieve a silky consistency.
Coat the pasta and bake: In a large oven-safe pot, combine the cooked pasta with the garlic and red pepper mixture. Add the pumpkin cheese sauce and stir until all the pasta is well coated. Stir in half the vegan mozzarella. Smooth over the top of the pasta and then Top with the remaining vegan mozzarella and bake covered for 20 minutes, until the pasta has softened and the cheese is melted.
Grill / Broil the top: Uncover the pot and grill / broil for 2–6 minutes until the top is gently browned. Keep a close eye to avoid burning. Let cool slightly, then top with fresh thyme leaves before serving.