Preheat your oven to 300°F (150°C). Pat the beef brisket dry with paper towels and place it on a large cutting board or tray.
In a small bowl, combine 1.5 teaspoons of kosher salt, 1.5 teaspoons of freshly ground black pepper, smoked paprika, garlic powder, onion powder, and dried thyme. Mix well to create a dry rub.
Rub the spice mixture all over the beef brisket, coating all sides evenly and pressing it gently into the meat so it adheres.
Heat 2 tablespoons of olive oil in a large oven-safe pot or Dutch oven over medium-high heat. When the oil is hot, add the brisket and sear for 3–4 minutes per side until deeply browned on all surfaces. Transfer the seared brisket to a plate.
Reduce the heat to medium, then add the sliced yellow onion to the same pot. Cook, stirring occasionally, for about 5 minutes until softened and lightly browned.
Stir in the minced garlic and cook for 30 seconds until fragrant, being careful not to let it burn.
Pour in the beef broth, barbecue sauce, and Worcestershire sauce, scraping the bottom of the pot with a spoon to release any browned bits.
Return the seared brisket to the pot, nestling it into the onion and liquid mixture. Cover the pot with a tight-fitting lid, transfer to the preheated oven, and bake for 2.5 to 3 hours, or until the brisket is very tender when pierced with a fork.
When the brisket is almost done, bring a large pot of salted water to a boil. Add the elbow macaroni and cook for 1–2 minutes less than the package directions for al dente. Drain the pasta and set aside.
While the pasta cooks, melt the unsalted butter in a medium saucepan over medium heat. Sprinkle in the all-purpose flour and whisk constantly for 1–2 minutes to form a smooth roux without browning it too much.
Gradually pour in the whole milk and heavy cream while whisking continuously to avoid lumps. Cook, stirring often, for 4–5 minutes until the mixture thickens slightly and gently bubbles.
Stir in the ground mustard, ground nutmeg, 0.5 teaspoon black pepper, and remaining 0.5 teaspoon kosher salt. Mix well to season the sauce evenly.
Reduce the heat to low and add the shredded sharp cheddar cheese, shredded mozzarella cheese, and grated Parmesan cheese in small handfuls, stirring after each addition until fully melted and smooth.
Combine the drained elbow macaroni with the cheese sauce in a large mixing bowl, stirring until all the pasta is well coated and creamy.
Transfer the mac and cheese mixture to a lightly greased baking dish, spreading it into an even layer.
In a small bowl, toss the panko breadcrumbs with 1 tablespoon of olive oil until the crumbs are lightly coated. Sprinkle the breadcrumb mixture evenly over the top of the mac and cheese.
Increase the oven temperature to 350°F (175°C). Place the baking dish in the oven and bake for 20–25 minutes, or until the top is golden and the edges are bubbling.
When the brisket is tender, remove the pot from the oven and let the meat rest in the cooking liquid for at least 10–15 minutes. Then transfer the brisket to a cutting board and slice it thinly against the grain.
To serve, scoop generous portions of the baked mac and cheese onto plates and top with slices of brisket. Spoon a little of the onion and pan juices from the pot over the brisket for extra flavor, and enjoy warm.