01 - Preheat the oven to 400°F. Line a rimmed baking sheet with parchment paper and set aside.
02 - Using a sharp knife, halve the spaghetti squash lengthwise. Scoop out and discard the seeds. Place both halves cut side down on the prepared baking sheet. Roast for 35 to 40 minutes until the flesh is fork-tender and separates easily into strands.
03 - While the squash roasts, melt the butter in a medium saucepan over medium heat. Whisk in the gluten-free flour and cook, stirring continuously, for 1 minute to form a smooth roux.
04 - Gradually pour in the whole milk while whisking vigorously to prevent lumps. Stir in the Dijon mustard, garlic powder, onion powder, salt, and black pepper. Continue cooking, stirring constantly, until the sauce thickens and coats the back of a spoon, about 3 to 4 minutes.
05 - Remove the saucepan from heat. Add the shredded sharp cheddar and Gruyère cheeses, stirring until fully melted and the sauce is smooth and glossy.
06 - Once the roasted squash is cool enough to handle, run a fork through the flesh to separate it into spaghetti-like strands. Discard the skins.
07 - Transfer the spaghetti squash strands into the cheese sauce and toss gently until every strand is evenly coated. Spoon the mixture into a greased 9×13-inch baking dish, spreading it into an even layer.
08 - In a small bowl, combine the gluten-free breadcrumbs, grated Parmesan, and melted butter. Mix until the crumbs are evenly moistened. Sprinkle the mixture uniformly over the squash casserole.
09 - Bake at 400°F for 10 minutes, or until the topping is golden brown and the edges are bubbling. Garnish with chopped fresh parsley and serve immediately.