Preheat your oven to 400°F (200°C). Carefully slice the spaghetti squash in half lengthwise, scoop out the seeds, brush the insides with melted butter, and sprinkle with salt and pepper.

Place the spaghetti squash halves cut-side down on a parchment-lined baking sheet. Roast in the oven for 45-60 minutes until tender.

Once cool enough to handle, use a fork to shred the squash flesh into strands. Set aside in a large bowl.

In a medium saucepan over medium heat, melt the remaining butter, add the diced onion, and sauté until translucent, about 4-5 minutes. Then add minced garlic and sauté for an additional minute.

Sprinkle the flour over the onion and garlic mixture, stirring continuously for about 1-2 minutes. Slowly whisk in the whole milk until smooth.

Bring the sauce to a simmer, stirring frequently until it thickens, about 3-5 minutes. Stir in salt, black pepper, and nutmeg if using. Fold in Gruyere and sharp cheddar cheese.

Pour the creamy cheese sauce over the shredded spaghetti squash and mix until evenly coated. Transfer to a greased baking dish.

In a small bowl, mix the reserved cheeses with panko breadcrumbs and sprinkle over the squash mixture.

Bake in the preheated oven for 20-25 minutes until the top is golden brown and bubbly.

Allow to rest for 5-10 minutes before serving. Garnish with freshly chopped parsley.