Preheat oven to 350°F. Add oil and onions to a large dutch oven and bring to medium-high heat. Season with a sprinkling of salt and pepper. Sauté for a good 10 minutes, stirring often, until the onions are golden brown and slightly dark around the edges.
Reduce heat to medium and add the sausage and garlic. Break up the sausage into a crumbly texture. Cook for a few minutes, stirring often, to caramelize the garlic and brown the meat. Add the paprika, chipotle chili powder, pinch cayenne, onion powder, garlic powder, nutritional yeast, thyme, sage, and oregano. Cook for a few more minutes to toast the herbs, stirring often.
At this point the mixture should smell outrageously good. Pour in the canned tomatoes, cheese, tamari, and sea salt. Mix well and continue to cook for about 7-8 minutes to bring the mixture to light simmer. Make sure to stir often so the bottom doesn’t burn. Once to a simmer, add the pasta noodles and 2 cups of water (this will just barley cover the pasta). Mix well and place the lid on top. Bake for 30 minutes.
Carefully remove from oven and take off the lid. Mix well. By now, all of the cheese should be melted and the pasta should be very close to being done! At this point you can taste a little bit and adjust the seasonings to your liking. Sprinkle on the crispy onions and some shredded vegan parmesan. Bake uncovered for an additional 15 minutes or until the top is crunchy and bubbly and the pasta noodles are thoroughly cooked. Remove from oven and let stand for a bit as it will be hot! Serve.