Start by heating your skillet over medium‑heat and adding the ground beef, chopped onion and Italian seasoning. Cook until the beef is nicely browned and the onion has softened. Then pour in the marinara sauce, add the basil pesto, sun‑dried tomatoes and chili paste or flakes, and let it all simmer for about five minutes to blend the flavors. Season with salt and pepper to taste.
While the red sauce simmers, in a glass measuring cup whisk together the cream cheese and half of the heavy cream until smooth. Then stir in the remaining cream, fresh thyme, nutmeg and shredded mozzarella. Season lightly with salt and pepper—this sauce will form the creamy layer inside the squash.
Place your small spaghetti squash with the tops cut off (or halved, seeded) on a sheet pan or roasting pan. Spoon the meat sauce into each squash, then pour over the cream sauce. Roast in a 425°F oven until the squash is tender (about 20‑30 minutes). Remove from the oven, sprinkle the provolone and Parmesan over each, then arrange butter slices, garlic cloves and sage leaves around the squash. Return to the oven and bake another 10‑15 minutes or until the cheese is beautifully golden.
Once out of the oven, remove the garlic cloves, chop them gently and then mix the chopped garlic with softened butter and sage leaves. Spread this fragrant mixture over the squash, then use a fork to scrape the inside of each squash into spaghetti‑like strands, mixing those with the melted cheese layer. Serve immediately while warm and gooey.