Warm 1 tablespoon of olive oil in a large skillet over medium heat. Add the chopped bacon and cook, stirring occasionally, until the bacon is crisp and the fat has rendered, about 5–7 minutes. Transfer the cooked bacon to the crock pot, leaving the drippings in the skillet.
Pat the beef chuck cubes dry with paper towels, then season them evenly with the kosher salt and freshly ground black pepper. Place the all-purpose flour in a shallow dish and lightly coat the seasoned beef cubes in the flour, shaking off any excess.
Add another 1 tablespoon of olive oil to the skillet if needed and increase the heat to medium-high. Brown the floured beef in batches, turning the pieces so they develop a deep brown crust on at least two sides, about 3–4 minutes per batch. Do not overcrowd the pan. Transfer each browned batch of beef to the crock pot on top of the bacon.
Reduce the skillet heat to medium and pour in 1/2 cup of the dry red wine. Use a wooden spoon to scrape up the browned bits from the bottom of the pan, letting the wine simmer for 1–2 minutes. Pour this deglazed mixture over the beef and bacon in the crock pot.
In a mixing bowl, whisk together the remaining 1 1/2 cups of dry red wine, the low-sodium beef broth, tomato paste, minced garlic, and dried thyme until the tomato paste is fully dissolved.
Add the sliced carrots and chopped yellow onion to the crock pot, spreading them evenly around the beef. Pour the wine and broth mixture over the top, then tuck in the bay leaves so they are submerged in the liquid.
Cover the crock pot with its lid and cook the beef bourguignon on LOW for 8 hours, or on HIGH for 4–5 hours, until the beef is very tender and the vegetables are soft.
About 30 minutes before serving, heat the remaining 1 tablespoon of olive oil and the unsalted butter in a large skillet over medium heat. Add the quartered mushrooms and cook, stirring occasionally, until they are golden brown and have released and reabsorbed their moisture, about 8–10 minutes.
Stir the browned mushrooms into the crock pot, re-cover, and let the beef bourguignon cook on LOW for an additional 20–30 minutes so the flavors can meld.
Remove the bay leaves from the crock pot and discard them. Taste the sauce and adjust the seasoning with a little more salt and pepper if needed. Ladle the beef bourguignon into bowls and sprinkle with the chopped fresh parsley before serving.