Bring a large saucepan of water to the boil and add the butternut squash chunks. Cook for 6-8 minutes until soft, then remove with a slotted spoon, (saving the water to boil the pasta in later).
Meanwhile, heat the oil in a large frying pan. Finely chop the onion and add to the pan, followed by the garlic. Cook gently for 3-4 minutes until soft, then stir through the flour and paprika and cook for a further minute.
Stir the milk into the frying pan, adding a little at a time and stirring as you go. Add the butternut squash chunks and cook for a further 2 minutes.
Add the pasta to the saucepan of water and boil for 8-10 minutes until soft.
Preheat the oven to 180°C / 350°F / Gas Mark 4.
Add the vegan cheese or nutritional yeast, mustard, salt and juice of half the lemon to the frying pan, then tip everything into a blender (or use a hand-blender in the pan), and blitz to a very smooth sauce.
When the pasta is cooked, drain it and return to the saucepan, then tip in the sauce and stir through to fully coat the pasta.
Tip the pasta into a large ovenproof dish, scatter with the breadcrumbs and vegan cheese then bake for 10-12 minutes until crispy and golden brown.