Preheat oven to 400°F (200°C).

Cut spaghetti squash in half lengthwise. Scoop out seeds and stringy bits.

Drizzle cut sides of squash with 2 tablespoons melted butter. Sprinkle generously with salt and pepper.

Place squash halves cut-side down on baking sheet lined with parchment paper. Roast for 45-60 minutes, or until squash is easily pierced with fork and flesh is tender.

Once cool enough to handle, use fork to shred flesh into spaghetti-like strands. Set aside.

In large saucepan over medium heat, melt remaining 2 tablespoons butter.

Add chopped onion to melted butter and cook until softened and translucent, about 5-7 minutes. Add minced garlic and cook for another minute until fragrant.

Sprinkle flour over onion and garlic mixture. Cook, stirring constantly, for 1-2 minutes to create roux.

Gradually whisk in milk, a little at a time, ensuring no lumps. Continue whisking until sauce is smooth.

Bring sauce to simmer over medium heat, stirring constantly. Reduce heat to low and simmer for 5-7 minutes until sauce has thickened slightly.

Stir in salt, pepper, and nutmeg. Taste and adjust seasonings as needed.

Remove saucepan from heat. Stir in 3/4 cup Gruyere cheese, 3/4 cup cheddar cheese, and 1/4 cup Parmesan cheese until melted and sauce is smooth and creamy. Reserve remaining cheese for topping.

Add shredded spaghetti squash to cheese sauce and stir gently to combine.

Pour spaghetti squash mixture into greased 9x13 inch baking dish.

In small bowl, combine remaining 1/4 cup Gruyere cheese, 1/4 cup cheddar cheese, 1/4 cup Parmesan cheese, and panko breadcrumbs.

Sprinkle cheese and breadcrumb mixture evenly over top of spaghetti squash.

Bake for 20-25 minutes, or until topping is golden brown and bubbly.

Remove from oven and let rest for 5-10 minutes before serving.

Garnish with chopped fresh parsley if desired. Serve hot.