Preheat your oven to 200°C (390°F). Find a sturdy baking dish, about 30x20cm, ready for assembling.
Cook the penne in a large pot of boiling salted water until just al dente, about 1 minute less than package instructions. Drain and toss with a drizzle of olive oil to prevent sticking.
Heat olive oil in a deep skillet over medium heat. Add chopped onions and cook until translucent and fragrant, about 3 minutes.
Add sliced mushrooms and minced garlic to the skillet. Sauté until the mushrooms are browned and fragrant, about 8 minutes, stirring occasionally.
Stir in the tomato sauce, nutritional yeast, smoked paprika, and season with salt and pepper. Let the mixture simmer for 5 minutes, until slightly thickened.
Combine the cooked pasta with the mushroom sauce mixture in the skillet, folding gently to coat evenly.
Transfer the pasta mixture into the prepared baking dish. Top with slices or shreds of vegan cheese and sprinkle a little extra nutritional yeast if desired.
Bake in the oven for 20-25 minutes until the top is golden and bubbling, with a slightly crisp edge.
Remove from the oven and let rest for 5 minutes. This helps the sauce thicken and makes slicing easier.
Slice into portions, serve hot, and enjoy the cheesy, smoky aroma and tender pasta with a crispy top.