Preheat your oven to 180°C (350°F) and lightly grease an 8×11-inch (or 9×9-inch) baking dish with a little olive oil.
Cook the pasta in a large pot of salted boiling water until just al dente—about 2 minutes less than the package instructions. Drain well and set aside. (Chef's Tip: Do not rinse the pasta; the natural starches help the sauce stick!) While the pasta cooks, heat 2 tablespoons of olive oil in a large, deep skillet or Dutch oven over medium heat. Add the chopped onion and cook until translucent and fragrant, about 5 minutes. Add the minced garlic and cook for 1 more minute, stirring constantly so it doesn't burn.
Sprinkle 2 tablespoons of all-purpose flour evenly over the onions and garlic. Stir constantly for 1 to 2 minutes. The mixture will look like a thick paste; cooking it now ensures your final sauce doesn't taste like raw flour.
Slowly pour the 2 ½ cups of plant-based milk into the skillet while whisking vigorously to prevent any lumps from forming. Bring the mixture to a gentle simmer over medium-low heat.
Stir in the nutritional yeast, lemon juice, and smoked paprika. Season generously with salt and black pepper to taste. Let the sauce simmer gently for 3 to 4 minutes, stirring frequently, until it thickens into a rich, velvety consistency.
Turn off the heat. Add the cooked, drained pasta directly into the deep skillet with the sauce. Toss gently using a wooden spoon or spatula until every piece of pasta is beautifully coated.
Transfer the coated pasta into your prepared baking dish, spreading it out evenly. In a small bowl, mix the ¼ cup of plant-based cheese and ¼ cup of breadcrumbs together, then sprinkle this mixture evenly over the top.
Bake uncovered for 20–25 minutes, until the sauce is bubbling around the edges and the cheese-and-breadcrumb topping has turned a beautiful crisp, golden brown.
Remove from the oven and let the pasta bake rest for 5 minutes before serving. This crucial step allows the dairy-free sauce to set so it doesn't run all over the plate.
Garnish with fresh herbs if desired, then serve hot and enjoy the rich, cheesy flavor and satisfying texture.