While the acorn squash is roasting, in a dutch oven over medium/high heat, add in the 3 tablespoons of olive oil and the Italian sausage. Fully cook the sausage through, about 8 minutes. Using a slotted spoon, remove the sausage and leave the oils/small bits in the pan. Set the sausage aside.
Lower the heat to medium, add in the diced onion and celery, sauté for 4 minutes until they begin to soften. Add in the apples, sage, thyme, garlic, a pinch of kosher salt, fresh ground black pepper, and crushed red pepper flakes. Sauté for 4 minutes. Return the sausage back into the dutch oven with the vegetables and stir to combine. Allow flavors to meld for 3 minutes.
Using a spoon, evenly add the stuffing into the acorn squashes.
In a small bowl, mix together the panko bread crumbs and parmesan cheese. Sprinkle over the top of each acorn squash.
Place the stuffed squashes into the oven for 15 minutes. The breadcrumbs/parmesan should be toasted brown. Remove from the oven and serve.