Make pasta according to package & preheat oven to 350 degrees F.
In a large skillet, add butternut squash and 2 cups of water. Bring to a low boil, cook covered for 5-7 minutes, or until butternut squash soften. Drain any water, add 1 tbsp oil, onion and garlic. Saute until onion is translucent.
Blend together butternut squash/onion mixture with milk until smooth.
In the same skillet, melt butter over medium low heat. Add arrowroot flour and stir until combined. Add in butternut squash sauce and salt, pepper, red pepper flakes. Simmer and stir until the sauce begins to thicken. Add 1/2 cup goats milk gouda and stir until melted.
In a 2 qt casserole dish (or baking dish of similar size), mix together cooked pasta and butternut squash sauce. If using bacon, add about 1/2 to the pasta.
Sprinkle with remaining cheese and bacon. Bake for 25-30 minutes or until cheese is golden brown.