Prep the Oven and Baking Dish: Preheat your oven to 375°F (190°C). Lightly grease a 9x13 inch (or similarly sized 3-quart) baking dish.

Braise the Greens: In a large Dutch oven or stockpot, render the diced bacon over medium heat until crispy. Remove the bacon with a slotted spoon and set aside, leaving the fat in the pot.

Sauté Aromatics: Add the diced yellow onion to the bacon fat and sauté for 5 to 7 minutes until softened and translucent. Add the minced garlic and red pepper flakes (if using), and cook for 1 minute until fragrant.

Cook the Collards: Add the chopped collard greens to the pot. They will fill the pot completely, but will wilt quickly. Cook for 5 minutes, stirring often, until they begin to collapse.

Braise: Pour in the 4 cups of chicken or vegetable stock and the apple cider vinegar. Bring the mixture to a simmer, then cover the pot and reduce the heat to low. Let the greens braise for 45 minutes to 1 hour, or until they are very tender.

Drain Thoroughly: Drain the cooked collards completely using a large colander, pressing down firmly with the back of a spoon to remove as much liquid as possible. It is crucial the greens are dry so the final gratin is not watery. Set the drained greens aside in a large bowl.

Make the Roux: In a medium saucepan, melt the 4 tablespoons of butter over medium heat. Whisk in the flour and cook, stirring constantly, for 2 minutes to cook out the raw flour taste. This creates your roux.

Add Milk: Gradually whisk in the warm milk, adding about a cup at a time, ensuring all lumps are dissolved before adding the next batch. Continue whisking constantly until the sauce thickens significantly, usually about 8 to 10 minutes, until it coats the back of a spoon.

Season and Add Cheese: Remove the saucepan from the heat. Stir in the Kosher salt, black pepper, and nutmeg. Add the shredded sharp cheddar, Gruyère, and the cubed cream cheese. Stir gently until all the cheese has melted completely and the sauce is smooth, creamy, and velvety.

Combine: Pour the finished cheese sauce over the drained collard greens in the large bowl. Add the reserved crispy bacon bits (if using). Toss gently until the greens are thoroughly coated with the sauce.

Transfer to Dish: Pour the collard green and cheese mixture into the prepared 9x13 inch baking dish, spreading it into an even layer.

Prepare Topping: In a small bowl, combine the Panko breadcrumbs, melted butter, and grated Parmesan cheese. Toss until the breadcrumbs are evenly coated.

Final Bake: Sprinkle the Panko topping evenly over the collard greens mixture. Bake for 25 to 30 minutes, or until the sauce is bubbly around the edges and the breadcrumb topping is golden brown and crisp.

Rest and Serve: Allow the gratin to rest for 10 minutes before slicing and serving so the sauce can fully set.