Preheat the oven to 425 degrees F. Slice off the neck portion of butternut squash that weighs about half a pound. Peel. There shouldn't be any seeds in this portion, but if there are, remove them. Chop up the squash into 1" pieces, place on a parchment paper lined baking sheet, toss in a little olive oil, and roast until soft and slightly caramelized.
Sauté the apple in a little butter over medium heat until soft.
Combine the squash, apple, cheeses and salt in the bowl of a food processor fitted with a blade, and purée.
Making the Brown Butter Pears and Balsamic Drizzle
Melt the butter in a pan over medium heat. Do not use a coated or dark pan, as it will be difficult to track the changing color of the butter as it browns. This frequently translates into burned butter. The butter will melt and start to bubble. Soon, the bubbling activity will dissipate and the butter will start to brown. I brown mine to a deep golden color for this dish.
Add the pears and sauté in the browned butter until just soft.
Follow the directions here to make the balsamic reduction.
Spoon the pears and browned butter over the pasta.
Drizzle 1 - 2 teaspoons of balsamic reduction over each serving (or more, to taste).
Sprinkle grated Parmesan cheese and fresh thyme over the top. Serve warm.