Preheat the oven to 425°F.
Line a baking sheet with parchment paper or aluminum foil.
Slice each butternut squash in half lengthwise.
Remove the seeds and stringy fibers from each squash half.
Drizzle the cut sides of the squash with olive oil.
Season the squash generously with kosher salt and freshly ground black pepper.
Place the squash halves cut-side down on the prepared baking sheet.
Roast for approximately 40 minutes, or until the squash is tender when pierced with a fork.
While the squash is roasting, add approximately 1 tbsp olive oil to a large skillet and place it over medium heat.
Add the bulk Italian sausage to the skillet.
Cook the sausage, breaking it apart as it browns, until fully cooked.
Transfer the cooked sausage to a large mixing bowl and set aside.
Add additional olive oil to the skillet if needed.
Add the sliced fennel and onion to the skillet.
Cook for approximately 10 minutes, stirring occasionally, until softened and lightly golden.
Add the cubed Honeycrisp apples, minced garlic, minced sage, and fresh thyme.
Continue cooking for several minutes, until the apples begin to soften and the garlic is fragrant.
Drizzle the mixture with maple syrup.
Season with kosher salt and freshly ground black pepper to taste.
Transfer the fennel, onion, and apple mixture to the bowl with the cooked sausage.
Stir until evenly combined.
Remove the roasted squash from the oven and allow it to cool until it can be handled safely.
Using a spoon, scoop out some of the cooked squash flesh, leaving approximately a 3/4-inch border around the sides and bottom of each squash half.
Chop the removed squash flesh, if necessary.
Add the squash flesh to the sausage and apple mixture.
Stir until the squash is evenly incorporated into the filling.
Spoon the filling evenly into the hollowed squash halves.
Sprinkle the grated Gruyere cheese over the filled squash halves.
Garnish with additional chopped sage, if desired.
Return the stuffed squash to the oven.
Bake for approximately 20 minutes, or until the cheese is melted, bubbly, and lightly golden.
Remove from the oven and allow the stuffed squash to rest for several minutes before serving.
Serve warm.