Grease a 9-by-13-inch baking pan with butter. Preheat the oven to 350 degrees F.
Put 4 cups of water into a pot and set over medium-high heat. Slowly whisk in the polenta so no lumps form. Add a big pinch of salt. Cook, stirring often, until the mixture comes to a boil. Lower the heat and cook according to the package directions. When it is finished, stir in the butter and 1/4 cup of the Parmesan.
Spread a cup of the Slow-Cooker Bolognese in the bottom of the prepared baking pan. Add half the polenta and spread it evenly over the sauce. Add a layer of 6 slices provolone and 3/4 cup mozzarella, then top with 2 cups of the sauce. Make another layer with the remaining polenta. Top with the remaining provolone, 3/4 cup mozzarella and remaining sauce. Sprinkle over the rest of the mozzarella and Parmesan.
Cover with foil and bake for 30 minutes. Remove the foil and continue baking until the cheese is browned and bubbling, about 15 minutes more. Let rest for 20 minutes before serving.
Heat 2 tablespoons of the oil in a large skillet over medium heat. Add the celery, carrots and onions, season with salt and pepper and cook until softened, about 10 minutes. Stir in the garlic and cook for 30 seconds. Add the tomato paste and cook for a minute. Pour in the red wine and cook until it is mostly evaporated, about 3 minutes. Pour this mixture into a slow cooker.
Pour the remaining 2 tablespoons oil into the skillet, add the beef and season with salt and pepper. Cook, breaking up any lumps, until it is nicely browned, about 15 minutes. Drain off any excess fat. Stir in the milk and cook until it is mostly absorbed by the meat, about 5 minutes. Add this to the slow cooker along with the tomatoes, oregano, basil, thyme, red pepper flakes, nutmeg and Parmesan rind if using. Add some salt. Give it a good stir, cover and cook on low for 6 hours.
Skim off any fat on top and check the consistency. If it is too thick, add a bit of water. If it is too thin, cook for another 30 minutes with the cover off.