1. Preheat your oven to 400°F (200°C), scrub potatoes clean, pat dry, and pierce them several times with a fork. Bake the potatoes directly on the oven rack for 45-60 minutes until tender.
2. Cook bacon in a large skillet over medium heat until crispy. Use a slotted spoon to transfer the bacon to a paper towel-lined plate and set aside. Reserve a few tablespoons of bacon grease if desired.
3. Allow baked potatoes to cool after removing them from the oven, then scoop out the flesh, leaving a small border inside the skins. Reserve the skins for garnishing if you wish.
4. In a large stockpot or Dutch oven, melt butter over medium heat, then add chopped yellow onion. Sauté until translucent, about 5 minutes.
5. Add minced garlic to the onions and cook for an additional 1-2 minutes, stirring continuously to prevent burning.
6. Sprinkle all-purpose flour over the onion and garlic, stirring continuously to form a roux, ensuring there are no lumps.
7. Gradually whisk chicken stock into the roux, stirring until smooth, and bring the mixture to a gentle simmer.
8. Add milk to the stock mixture, stirring regularly as the soup begins to thicken. Let it cook for about 10-15 minutes.
9. Add the scooped-out potato flesh into the soup, using a fork or potato masher to break up larger chunks, creating a slightly chunky texture.
10. Season the soup with salt and pepper to taste, and adjust according to your preference.
11. Lower the heat and stir sour cream and shredded cheddar cheese into the soup until melted and creamy.
12. Serve the soup hot and garnish with crispy bacon, scallions or chives, shredded cheese, and reserved crispy potato skins for added texture and flavor.