Season the chuck roast pieces generously with kosher salt on every side. Large pieces of meat need plenty of salt.
Heat the oil in a large dutch oven over medium-high heat. Place the chuck roast into the pot and allow it to sear on each side, using tongs to flip them. PRO TIP: the beef will release itself from the pan once it's done searing on that side. If it doesn't lift, don't force it, just wait.
Once all sides are seared a deep brown, remove the beef to a plate and set aside.
Turn the heat down to medium, then sauté the onions, carrots, and celery for 5 minutes or until translucent and starting to turn golden brown, stirring with a wooden spoon frequently. Add the garlic, thyme leaves, and basil to the pot and let cook for another 1-2 minutes.
Add the seared chuck roast and the accumulated juices back to the pot.
Deglaze the dutch oven with a cup of beef broth, scraping the bottom with a wooden spoon to incorporate the fond. Pour in the rest of the beef broth, red pepper flakes (if using), canned tomatoes, the parmesan rind, and bay leaves. Let the ragu sauce come to a lively simmer, stirring occasionally.
Once it comes to a simmer, cover the pot with a lid, turn the heat down to low, and let cook for 2 ½ to 4 hours or until the meat easily shreds with a fork, stirring every so often to make sure nothing burns on the bottom. You can also place the covered pot into a 325 degrees F (165 degrees C) oven for the same amount of time.
Give a taste and season with more kosher salt and freshly ground black pepper if needed. Skim any excess fat off the top of the ragu, if desired, and remove the parmesan rind, bay leaves, and basil leaves before serving.
Serve the beef ragu hot over cooked pappardelle pasta, with a few leaves of basil and freshly grated parmesan.