Roast the Peppers: Preheat oven to 450°F (230°C). Roast whole red peppers for 25–30 minutes until skins are charred. Cover with a bowl or plastic wrap for 10 minutes, then peel.
Cook Pasta: Boil penne in salted water according to package instructions. Drain and reserve ½ cup pasta water.
Prepare Sauce: Heat olive oil in a pan, sauté onion and garlic until soft.
Blend Sauce: In a blender, combine roasted peppers, sautéed onion and garlic, almond milk, nutritional yeast, lemon juice, smoked paprika, and chili flakes. Blend until smooth.
Combine: Pour sauce back into the pan, warm over medium heat. Adjust salt and pepper. Add pasta and toss to coat evenly. Use reserved pasta water if needed to loosen sauce.
Optional Toppings: Add tofu, garnish with basil or parsley, sprinkle with pine nuts. Serve warm.