Heat the oven to 350°F. Lightly grease a 9-by-13-inch baking dish if you will be transferring the bean mixture from the skillet or Dutch oven.

Cook the chopped bacon in a large oven-safe skillet or Dutch oven over medium heat for 6 to 8 minutes, until partly crisp and most of the fat has rendered. Add the diced onion and cook for 4 to 5 minutes, until softened.

Drain off excess bacon fat, leaving approximately 1 tablespoon in the pan. Keeping a little fat preserves the smoky flavor and gives the onions and sauce a savory foundation.

Stir in the beans and their sauce, brown sugar, ketchup, molasses, yellow mustard, apple-cider vinegar, black pepper, and optional smoked paprika or cayenne. Mix thoroughly so the sweet and tangy ingredients are evenly distributed.

Bring the mixture to a gentle simmer on the stovetop for 2 to 3 minutes. This warms the sauce and gives the flavors a chance to begin blending before the casserole enters the oven.

If you are not using an oven-safe skillet or Dutch oven, transfer the mixture to the lightly greased 9-by-13-inch baking dish. Spread it into an even layer so it cooks consistently.

Bake uncovered at 350°F for 45 to 60 minutes, until the beans are bubbling around the edges and the sauce has thickened. Stir once halfway through if the edges begin browning too quickly.

Let the baked beans stand for 10 minutes before serving. The sauce thickens as it rests, making the beans easier to spoon and helping the brown sugar and molasses glaze cling to them.