Pat the pork shoulder dry and sprinkle all sides of the meat with salt and pepper. Select the sauté function on the Instant Pot and drizzle in the olive oil. When the pot is hot, add the meat and sear for 2 to 3 minutes on each side or until well browned. Remove the meat to a plate. Add the onion and red pepper flakes to the Instant Pot and cook, stirring often, until the onion is soft and translucent. If the bottom of the pot begins to burn while the onion is cooking, add a small splash of water. Next add the white wine and cook until it has evaporated almost completely. Add the tomatoes and use the back of a spoon to break them up into bite-size pieces. Return the pork to the pot along with the sage bundle, garlic cloves, Parmesan rind, and ¾ cup of water. Put the lid on and cook on high pressure for 1 hour. Let the Instant Pot naturally depressurize for 5 to 10 minutes, then quick-release the remaining pressure. Remove the pork to a bowl and use a fork to shred it into bite-size pieces. It should be very tender. Cover the meat loosely with foil. Remove the sage bundle and Parmesan rind. Turn the Instant Pot to the sauté function and add the beans to the tomato sauce. Cook for 10 to 15 minutes, stirring occasionally, until the sauce has thickened a bit. Adjust the seasoning to taste; another teaspoon of salt is usually necessary. Return the pork to the pot and stir gently. Serve with polenta, pasta, or crusty bread. Store leftovers in an airtight container in the refrigerator for up to 3 days.