01 - Preheat oven to 400°F. Halve the spaghetti squash lengthwise and scoop out the seeds. Place cut side down on a parchment-lined baking sheet. Roast for 35–40 minutes until fork-tender and strands separate easily.
02 - In a medium saucepan over medium heat, melt the butter. Whisk in the gluten-free flour and cook for 1 minute, stirring constantly to form a smooth roux.
03 - Gradually pour in the whole milk while whisking continuously. Cook for 2–3 minutes until the mixture thickens to a silky consistency.
04 - Reduce heat to low and add the cheddar, Gruyère, garlic powder, ground mustard, salt, and black pepper. Stir until the cheeses melt completely and the sauce is smooth. Remove from heat.
05 - Once the squash is cool enough to handle, use a fork to scrape the flesh into long spaghetti-like strands. Transfer to a large mixing bowl and gently fold in the cheese sauce until evenly coated.
06 - Transfer the sauced squash to a lightly greased baking dish. Combine the breadcrumbs, Parmesan, and melted butter in a small bowl, then sprinkle evenly over the top. Bake at 400°F for 10–12 minutes until golden and bubbling.
07 - Scatter fresh chives or chopped parsley over the top and serve immediately while hot.