Preheat the oven to 400 degrees. Cut the squash into small cubes. Place the squash, onions, garlic, olive oil, and salt on a baking sheet and toss to coat the ingredients evenly. Roast for 30 minutes, tossing the vegetables once or twice, or until squash is fork tender. Remove the pan from the oven and let the vegetables cool. Reduce the oven temperature to 350 degrees. Place the roasted vegetables (or strained frozen puree), cream cheese, stock, and pepper in a food processor and process the ingredients for 2-3 minutes, or until smooth and thoroughly blended. Generously grease a large (9-inch x 13-inch) baking dish. Spoon 1/3 of the squash mixture on the bottom. Cover with matzo (break up the pieces, if necessary, to fit the pan). Sprinkle with 1/3 of the mozzarella cheese. Repeat the layers another two times. Sprinkle the top with the Parmesan cheese. Cover the dish with aluminum foil, slightly tented. Bake for 40 minutes. Remove the foil and bake for another 12-15 minutes or until the top is golden brown and bubbly. Let rest for 5-6 minutes before serving. Tip: you may use 4 cups thawed, pureed butternut squash instead of fresh. If you use frozen squash, let it thaw, then place in a strainer for about 15 minutes to drain excess liquid.