Bring a large pot of salted water to a boil and cook the pasta until just al dente, about 1 minute less than package instructions. Drain and set aside.
In the same pot or a sauté pan, heat olive oil over medium heat. Add chopped onions and sauté until they become translucent and fragrant, about 3-4 minutes.
Add minced garlic to the onions and cook for another minute until the garlic is fragrant, being careful not to burn it.
Pour in the canned crushed tomatoes, stirring well. Season with salt, pepper, and a pinch of chili flakes if desired. Let the sauce simmer gently for about 10 minutes until it thickens slightly and develops flavor.
Stir in the vegan cream and chopped fresh basil into the sauce, blending everything together until smooth and creamy.
Add the cooked pasta to the sauce, tossing gently to coat each piece evenly. Mix in the nutritional yeast for a cheesy flavor boost.
Transfer the pasta mixture into a greased baking dish, spreading it out evenly with the back of a spoon or spatula.
Sprinkle the top with additional nutritional yeast or vegan cheese for a cheesy crust.
Bake in a preheated oven at 180°C (356°F) for 20-25 minutes until bubbling around the edges and the top is golden brown.
Remove from the oven and let it rest for about 5 minutes to settle before serving. The top should be crispy and the sauce bubbling.
Serve hot, garnished with extra basil if desired, and enjoy this comforting, cheesy vegan pasta bake.