Heat oven to 375°F. Grease a 9-inch square baking dish.
Squeeze the thawed spinach completely dry with towels or a sieve.
Melt 2 tbsp butter in a skillet over medium heat. Soften onion for 4 minutes, then stir in garlic for 30 seconds. Let cool slightly.
Beat cream cheese in a large bowl until smooth. Mix in sour cream and the beaten eggs until creamy.
Season with salt, pepper, nutmeg, red pepper flakes, and lemon zest.
Fold in the drained spinach, sautéed onion mixture, 3/4 cup cheddar, and about 1/2 cup Parmesan.
Spread the mixture in the prepared dish. Melt the remaining 1 tbsp butter and toss with breadcrumbs.
Top casserole with remaining cheddar and Parmesan. Scatter the buttered breadcrumbs over the surface.
Bake 30–35 minutes until bubbling and deeply golden. Rest 10 minutes before serving.