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Heat a large (roughly 5-Quart) heavy-bottomed Dutch oven or pot over medium-low heat.
Add the olive oil and butter. Once the butter has melted, add the diced onions and ½ teaspoon Diamond Crystal kosher salt.
Sauté the onions, stirring often, until softened and nearly translucent, about 5 to 7 minutes.
Add the celery, carrots, and another pinch of salt. Cook for 2 to 3 minutes, stirring often.
Add the garlic and red pepper flakes, if using, and cook until fragrant, stirring constantly, about 1 minute or so.
Add the ground beef, a generous pinch of kosher salt, and freshly ground black pepper.
Cook over medium heat, breaking up the meat with a fork as needed, until nearly cooked through and no longer raw, about 3 to 5 minutes.
Add the milk and simmer over low heat, stirring frequently, until the milk has mostly cooked out, about 5 to 7 minutes.
Stir in the freshly grated nutmeg.
Add the white wine and simmer until evaporated, about 3 to 5 minutes.
Add the canned tomatoes and parmesan rinds and stir mixture to combine.
Bring to a slow boil, then reduce heat immediately to a very, very low simmer.
Simmer the sauce, uncovered, for at least 3 to 4 hours, stirring every so often.
Add a splash of water as needed throughout the simmer time.
Season to taste with salt and pepper, and remove and discard the parmesan rinds.