Cook the Pasta Shells:
Bring a large saucepan of water to a boil and generously salt the water. Add the jumbo pasta shells and cook according to the box instructions until just al dente. Do not overcook. Drain well.
Transfer the cooked pasta shells to a baking sheet, drizzle with 1 tablespoon olive oil to prevent sticking, and set aside.
Preheat the Oven:
Preheat the oven to 350°F (175°C). Prepare a 13×9-inch (33×23 cm) rectangular oven-safe baking dish.
Prepare the Tofu Ricotta:
Drain the block of tofu and pat away the excess water with paper towels. Place the tofu in a food processor. Add nutritional yeast, garlic powder, onion powder, 1 1/2 teaspoons kosher salt, black pepper, extra virgin olive oil, lemon zest, lemon juice, and crushed red pepper flakes.
Pulse repeatedly until the texture is relatively smooth but still a bit chunky, similar to ricotta cheese.
Make the Pumpkin Ricotta Filling:
In a large bowl, combine the Tofu Ricotta, pumpkin purée, nutmeg, and vegan parmesan cheese (if using). Fold the ingredients together using a silicone spatula.
Taste the filling and adjust the seasonings, adding more salt, pepper, or nutmeg as needed. Spoon 1-2 tablespoons of the filling into each jumbo pasta shell and set aside.
Make the Garlic Béchamel Sauce:
Heat a large frying pan over medium heat and add 3 tablespoons extra virgin olive oil. Once the oil is hot, add the diced onion and season with a pinch of salt. Cook for 6-7 minutes until the onion is softened and lightly browned.
Add the minced garlic and cook for 1-2 minutes, stirring frequently to prevent burning.
Reduce the heat to medium-low and add the flour, whisking constantly for a minute until well incorporated.
Gradually pour in the lite coconut milk in stages, whisking after each addition to prevent clumps. Cook for 2 minutes until the sauce has thickened.
Transfer the sauce to a blender, add 1 teaspoon kosher salt and black pepper to taste. Blend until smooth and creamy. Adjust seasonings as desired.
Assemble the Dish:
Pour 1/2 cup of the Garlic Béchamel Sauce into the baking dish to create a thin layer on the bottom.
Arrange the stuffed jumbo shells on top of the sauce. Pour the remaining sauce over the shells. Scatter the chopped fresh sage leaves on top.
Bake the stuffed shells for 22-25 minutes, or until the pasta shells are lightly golden. Serve warm.