In a small bowl, beat egg yolks and Parmesan together with a fork until they form a homogeneous thick paste, about 1 minute. Season with a few grindings of black pepper. Set aside.

In a large skillet, cook bacon over medium-low heat, stirring occasionally, until fat has rendered and bacon is golden brown and crisp, about 15 minutes. Remove from heat. Using slotted spoon, transfer bacon to a plate. Set aside.

Using clean hands, add sausage to skillet by pinching off 3/4- to 1-inch pieces and arranging in a single layer in the pan. Alternatively, add sausage to skillet all at once, then break up into pieces with a wooden spoon, spreading them out evenly in the pan. Cook over medium heat, undisturbed, until bottom side is light golden brown, about 1 minute. Add onion, season lightly with salt, and, using a thin metal spatula, turn sausage pieces onto uncooked side. Continue to cook, stirring occasionally, until sausage is cooked through, onion is softened, and fat in the pan is clear and no longer cloudy, 5 to 7 minutes; lower heat at any point if sausage or onion threaten to scorch.

Add pepper flakes (if using) and bloom in rendered fat until aromatic, about 30 seconds. Add tomato (finely chopped), season lightly with salt, and bring to a simmer. Cook, stirring occasionally, until sauce has thickened slightly and fat has emulsified into sauce, about 10 minutes.

Meanwhile, in a pot of lightly salted boiling water, cook pasta until softened on the exterior, but well shy of al dente, and still uncooked in the center (about 3 minutes less than the package directs). Using a spider skimmer, transfer pasta to sauce, along with 1/2 cup pasta cooking water. Transfer an additional 1/4 cup pasta cooking water to bowl with reserved egg yolk-Parmesan paste, and stir with a rubber spatula until smooth and well-combined; set aside. Alternatively, if you don't have a spider skimmer, drain pasta using a colander or fine-mesh strainer, making sure to reserve at least 1 1/2 cups pasta cooking water, before proceeding with above instructions.

Increase heat to high and cook, stirring and tossing rapidly, until pasta is al dente and sauce is thickened and coats noodles, about 2 minutes, adding more pasta cooking water in 1/4 cup increments as needed.

Remove skillet from heat, add cooked bacon and egg yolk mixture, and stir and toss rapidly until fully incorporated and pasta is glossy, 15 to 30 seconds. Season with salt and pepper to taste. Serve immediately, passing more grated cheese at the table.