Preheat oven to 350°F (180°C).
In a large oven-safe skillet with high sides or Dutch oven, cook 10 ounces bacon, chopped, over medium-low heat until the fat is melted (rendered) and it's slightly crisp and brown. Remove some fat if there’s too much, but keep about 2 tablespoons.
Add ½ cup diced onion and 1 garlic clove, minced, to the pot and sauté for 2–3 minutes, until softened and fragrant and lightly browned. Don't let it burn, or it might turn bitter.
Stir in 1 apple, peeled, cored and diced, and cook for a few more minutes.
Add ½ cup regular ketchup, 3 tablespoons apple cider vinegar, 1 tablespoon molasses, 1 or 2 tablespoons brown sugar (if using), 1 tablespoon Dijon mustard, ½ teaspoon ground cinnamon, and ¼ teaspoon ground nutmeg. Stir to combine.
Add 30 ounces navy or Great Northern beans, drained and rinsed, toss to mix, and season with ½ teaspoon salt and ⅛ teaspoon black pepper. At this point, it's hard to know if it will need more seasonings as their flavor concentrates during baking. So don't overdo it. You will adjust later.
Bake, uncovered, for 40–45 minutes, stirring twice during this time (don't forget the oven mitts!!), until the sauce thickens and bubbles gently. About 5-10 minutes before the time, when the preparation has thickened nicely, taste and adjust salt and pepper if needed.
Remove from the oven (use oven mitts as the pot is extremely hot!) and let it sit 10 minutes before serving; the sauce will thicken more. Taste and adjust seasonings if needed. If eating it the next day, see Notes below to cool it down.