Heat oven to 350°F. Grease a 2-quart baking dish.
Squeeze the thawed spinach very dry; set aside.
Melt 1 1/2 tbsp butter in a skillet. Soften onion over medium heat, 4–5 minutes. Stir in garlic for 30 seconds.
Beat cream cheese with sour cream until smooth. Season with salt, pepper, nutmeg, and red pepper flakes.
Fold in spinach, cooked onion mixture, 1 cup cheddar, and about 1/3 cup Parmesan.
Spread the mixture into the prepared dish.
Combine cracker crumbs with melted butter, remaining cheddar, and remaining Parmesan.
Sprinkle topping over the casserole and bake until bubbly and golden, 25–30 minutes. Rest 10 minutes before serving.