Start by preheating your oven to 350 degrees Fahrenheit. Place your cubed butternut squash into a large pot of boiling water and cook until the pieces are fork-tender, which usually takes about 15 to 20 minutes. Alternatively, you can roast the squash in the oven for a deeper, more caramelized flavor before proceeding to the next step.
Drain the cooked squash thoroughly and place it into a large mixing bowl. Use a potato masher or an electric hand mixer to blend the squash until it is smooth and free of large lumps. While the squash is still warm, add the melted butter, granulated sugar, salt, and alcohol-free vanilla, mixing until everything is fully incorporated.
Wait a minute for the mixture to cool slightly so the eggs do not scramble upon contact. Beat in the two eggs one at a time, ensuring the batter is light and fluffy. Once combined, pour the squash mixture into a greased 2 quart baking dish and spread it out evenly with a spatula.
In a small separate bowl, combine the brown sugar, flour, and chopped pecans. Use a fork or your fingers to work the softened butter into the dry ingredients until the mixture looks like coarse crumbs. Sprinkle this topping generously over the squash base, covering as much surface area as possible.
Place the casserole dish in the center rack of your oven and bake for 35 to 40 minutes. You will know it is done when the topping is a beautiful golden brown and the squash mixture is set around the edges. Let the dish rest for at least 10 minutes before serving to allow the flavors to settle and the texture to firm up.
