Season the short ribs with salt and pepper. Cook the bacon in a large skillet over medium heat until crisp, about 5 minutes. Remove the bacon. If there's excess bacon grease, drain off all but 1 tablespoon. Add the short ribs and sear on both sides. Remove the ribs and transfer to the slow cooker along with the bacon.
To the slow cooker, add the parmesan rind, wine, broth, tomatoes, tomato paste, onion, garlic, celery, carrot, thyme, sage, red pepper flakes, 4 tablespoons butter, and season with salt and pepper. Cover and cook on low for 6-8 hours.
Once done cooking, remove the short ribs, let cool slightly, then shred the meat and discard the bones, parmesan rind, and thyme. Add the shredded meat and parmesan, toss with the sauce. Keep on warm.
Bring a large pot of salted water to a boil. Cook the pasta according to package directions until al dente. Drain and toss the pasta with 4 tablespoons butter.
Divide the pasta between plates, add the ragù, and toss well. Top each serving with burrata and additional parmesan.