Preheat the oven to 475 degrees F.
Place the prepped spaghetti squash on a baking sheet, cut side up, and drizzle with olive oil, salt and pepper and roast until fork tender and easily shreddable, about 45-60 minutes. Remove and carefully shred the squash and transfer to a bowl
Heat the oil in a large nonstick cast iron skillet over medium-high heat. Add the onions and garlic and cook, stirring occasionally, until soft, about 5 minutes. Add the ground chicken and cook, stirring occasionally, until the chicken is cooked through and the onions are golden brown, 10 to 12 minutes. Remove from the heat and season with salt and pepper.
Add the spaghetti squash, marinara sauce and red pepper flakes to the skillet with the chicken mixture and stir to combine. Add the parmesan and stir.
Sprinkle with the mozzarella. Bake on the top oven rack until hot and bubbling and the cheese turns golden, about 15 minutes. Remove from the oven and let sit for 5 minutes. Add burrata on top. And season with salt and pepper as needed. Garnish with fresh herbs and serve