Preheat oven to 400°F and line a baking sheet with parchment paper.
Cut the butternut squash in half vertically and scoop out seeds. Drizzle with olive oil, sprinkle with salt and pepper, and place cut side-down on the baking sheet. Prick skin with a fork. Roast for 40 minutes.
Wrap the shallot, garlic cloves, and sage in foil with a drizzle of olive oil and pinch of salt. Place in the oven and roast for 20 minutes.
Allow the roasted squash, shallots, garlic, and sage to cool for at least 30 minutes.
Prepare homemade pasta dough according to your recipe instructions. Wrap dough and let it rest.
In a food processor, pulse walnuts until finely ground. Add the roasted shallots, garlic, sage, and 1½ packed cups of roasted squash. Add apple cider vinegar, nutmeg, sea salt, and black pepper. Pulse until smooth. Chill filling until ready to use.
Roll out pasta sheets, skipping folding steps. Place four sheets on a floured surface. Spoon filling in tablespoon-sized portions spaced on two sheets.
Lay the remaining two sheets over the filling. Press dough gently to seal around filling. Use ravioli stamp or cutter to cut shapes.
Cook ravioli in salted boiling water for 4 minutes, adding them as you begin preparing the sauce.
For the sauce, heat olive oil in a skillet over medium heat. Add sliced garlic and sage leaves; cook for 3 minutes.
Add white wine, fresh thyme leaves, and sea salt; cook while stirring for 2 minutes.
Serve ravioli topped with the sauce, chopped walnuts, freshly ground black pepper, and optional roasted squash cubes, sautéed kale, and grated pecorino.