In a large Dutch oven set over medium high heat, melt the butter, then add the onion with a generous pinch of salt and cook for 3 minutes, stirring frequently. Add the garlic and cook until it's fragrant, roughly a minute.
Sprinkle on the flour and cook for 2 minutes, whisking constantly.
Slowly pour in the chicken broth while whisking to prevent clumps. Pour in the milk and the heavy cream. Stir, then carefully add the potatoes to prevent splashing.
Cover and bring to a slight boil, which will take roughly 6 minutes. Reduce the heat to medium low. Keep covered and simmer for 8 minutes or until the potatoes are fork tender.
While it is cooking, fry the bacon in a cast iron skillet until it is golden brown. Transfer to a paper towel-lined plate and blot off any extra grease. Allow to cool, then crumble into smaller pieces.
Using a potato masher, mash the potatoes in the pot to help thicken the soup and to change the texture. Mash roughly half the potatoes. Stir in the sea salt, Tabasco, liquid smoke, and a pinch of turmeric if you want it to have a more golden hue.
Add the freshly grated Parmesan cheese, Neufchâtel cheese cubes, bacon crumbles, and chives. Whisk until the cheese melts, then simmer uncovered on medium low heat for 15 minutes. Taste and adjust seasonings, if necessary.
Garnish with additional toppings, such as bacon, chives, and Parmesan cheese. Serve in a sourdough bread bowl or in a bowl with a chunk of a French baguette or a wedge of black pepper focaccia. Panera also gives you the option of kettle chips or an apple with your order.