Preheat the oven to 425 degrees F. Place the squash on a plate and microwave 3 minutes. Let cool slightly, then cut in half lengthwise, scoop out the seeds and discard. Meanwhile, in a medium bowl, mix together the milk, pesto, oregano, spinach, and ricotta cheese. Season with red pepper flakes, salt and pepper. Stir in 1 cup fontina cheese and 1/2 cup provolone cheese. Place the squash in a baking dish and season the cut sides with salt and pepper. Sprinkle the remaining fontina cheese in the bottom of each squash, then evenly divide the milk mix among the squash cavities. Top with the remaining provolone cheese. Cover the squash loosely with foil. Transfer to the oven and bake 20 minutes. Remove the foil and continue baking another 15-20 minutes or until the squash is tender and the cheese is golden brown on top. The squash will seem a little soupy, this is OK. Let the squash sit 5 minutes, then use a fork to scrape the squash into strands, mixing the cheese with the squash. Serve topped with fresh oregano.: When you slide the dish into the oven you want an immediate burst of dry, hot air to start the browning process, which encourages the cheese to form a golden crust while the squash becomes tender. You should hear a faint hum of the oven as it settles at temperature, and the air will smell faintly warm and dry. A common mistake is not preheating long enough, which can extend bake time and yield less even browning; always wait until your oven fully reaches temperature.
Place the squash on a plate and microwave 3 minutes.: This quick blast helps soften the squash so cutting and scooping are easier, and you may notice steam rising when you remove it. The flesh will feel slightly warm and yielding to the touch. Avoid microwaving too long because the flesh can become overly soft and watery, making it harder to keep the cavity intact for stuffing.
Let cool slightly, then cut in half lengthwise, scoop out the seeds and discard.: Allowing the squash to cool makes handling safe and prevents burns, and when you cut lengthwise the interior will reveal the stringy flesh. Use a spoon to scrape and remove the seeds; they will be clustered at the center and should come away easily. A common error is rushing the cooling step, which can lead to slipping with the knife, so take a moment to let it rest.
Meanwhile, in a medium bowl, mix together the milk, pesto, oregano, spinach, and ricotta cheese.: As you whisk these elements you will see the creamy ricotta cheese and basil pesto combine into a glossy, slightly green filling, and the spinach will distribute color and earthy notes. The mixture should be cohesive but not watery; texture here determines how the filling bakes. Overmixing is a pitfall because it can break down the spinach and flatten the texture, so combine gently.
Season with red pepper flakes, salt and pepper.: Layering seasoning at this stage lets the heat and salt permeate the filling, creating depth. When you taste a small spoonful you should detect a hint of heat, balanced saltiness, and herb lift. Under seasoning is common, so taste and adjust carefully rather than adding too much at once.
Stir in 1 cup fontina cheese and 1/2 cup provolone cheese.: These melting cheeses will give the filling its luxurious stretch and body once baked, and their aroma becomes more pronounced as they approach room temperature in the mix. The texture will become slightly thicker and silkier. A mistake to avoid is using pre shredded cheeses with anti caking agents that can reduce meltiness; freshly shredded yields the best texture.
Place the squash in a baking dish and season the cut sides with salt and pepper.: Set the halves cut side up in a snug baking dish so they support the filling. Salting the cut surfaces brings out the squash sweetness and enhances the overall flavor. If your dish is too small the squash may tip and spill, so choose a pan that fits comfortably.
Sprinkle the remaining fontina cheese in the bottom of each squash, then evenly divide the milk mix among the squash cavities.: Adding a layer of fontina cheese at the base creates a molten cushion that helps the strands cling when you later scrape them. Distribute the filling so each half is generously but not overflowing. Overfilling is a common oversight that leads to an overly soupy bake, so leave a slight gap at the rim.
Top with the remaining provolone cheese.: The final blanket of provolone cheese forms a browning surface that will crisp in places and brown beautifully. Visually you should see a glossy cheese cap that will bubble and roast. Placing too much high moisture cheese on top can prevent proper browning, so keep the amounts as directed.
Cover the squash loosely with foil.: Tent the foil so it does not touch the cheese directly, creating a gentle steam environment that cooks the squash through. You should see little condensation form on the foil during baking, which indicates even cooking. Wrapping too tightly traps excess moisture against the cheese and can hinder browning after the foil is removed.
Transfer to the oven and bake 20 minutes.: During this first stage of baking the squash flesh will soften and the filling will heat through. You may smell the meld of basil pesto and cheeses as they warm. A common mistake is underbaking this phase, which can leave the center cool and the cheeses not fully integrated; rely on time and oven heat for a consistent result.
Remove the foil and continue baking another 15 to 20 minutes or until the squash is tender and the cheese is golden brown on top.: With the foil off, the cheese will brown and develop those toasty, caramelized spots you want. Listen for gentle bubbling, and look for a golden hue. If you pull it too early the cheeses will be melted but not browned; if you leave it too long the strands can dry out, so watch closely in the final minutes.
The squash will seem a little soupy, this is OK.: As the dish rests the liquid will settle into the squash strands, melding into a creamy sauce. You should notice a glossy sheen rather than watery separation. Trying to serve immediately while piping hot can make portions slide, so allow a short rest to let the texture stabilize.
Let the squash sit 5 minutes, then use a fork to scrape the squash into strands, mixing the cheese with the squash.: Resting allows the juices to settle and the cheese to firm slightly. When you scrape with a fork the strands will separate easily and mingle with the melted cheeses, creating a luxurious ribboned texture. A common trap is shredding too vigorously, which can smash the strands rather than lift them, so use gentle strokes.
Serve topped with fresh oregano.: A final scatter of fresh oregano adds bright herb aroma and a fresh finish that contrasts the warm, melted cheeses. The herb will steam slightly on contact with the hot squash, releasing fragrant oils. Avoid adding delicate garnishes too early, or they will wilt in the residual heat; add them just before serving.