Preheat the oven to 400°F (200°C) and gather parchment paper for lining the baking sheet.

Slice the spaghetti squash in half lengthwise, scoop out the seeds, season with butter, salt, and black pepper, then roast cut-side down for 45-60 minutes until tender.

Once roasted, shred the squash flesh into strands and set aside.

Melt 2 tablespoons of butter in a medium saucepan and sauté chopped onions until translucent. Stir in minced garlic and cook until fragrant.

Sprinkle flour over the onion and garlic mixture, stirring to combine, and cook for 1-2 minutes to create a roux.

Gradually whisk in whole milk, stirring until smooth. Bring to a simmer and cook for 5-7 minutes until thickened.

Reduce heat and stir in salt, pepper, nutmeg, and cheeses until melted and blended. Combine with shredded spaghetti squash.

Transfer the mixture to a greased baking dish, top with a mixture of panko breadcrumbs and additional cheese.

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

Let rest for 5-10 minutes before garnishing with fresh parsley and serving.