Preheat your oven to about 425°F (220°C). Toss the cubed butternut squash with 1 Tbsp olive oil, salt, pepper and thyme, then spread it in a single layer on your baking sheet. Roast until the squash is tender and edges are lightly caramelized—about 20 minutes.
While the squash roasts, cook your pasta in salted boiling water according to package instructions until al dente. Drain and set aside. In a skillet over medium heat, add the remaining olive oil and sauté the chopped onion until golden, then add the minced garlic and cook for an additional minute until fragrant.
To the skillet, add the roasted butternut squash, almond milk and balsamic vinegar and gently mash or break up some of the squash to create a creamy base. Stir in the chopped sage and parsley, then add the drained pasta and walnuts, tossing everything together so the sauce coats the pasta evenly. Season with salt and pepper, and serve immediately while warm.