Combine pinto beans, navy beans, and baking soda in a large pot. Add water until level is 2 inches higher than beans. Heat over medium-high heat until boiling. Cook for 5 minutes then remove pot from heat. Set aside to soak for 8 hours.

Drain beans, reserving 1 1/2 cups soaking liquid. Place beans in a slow cooker.

Place salt pork in a large skillet over high heat; sear until browned, 3 to 5 minutes per side. Remove from the heat, cut into small chunks, and add to the slow cooker.

Add onion to the skillet with the leftover pork fat; cook over medium-high heat until translucent, about 5 minutes; transfer to the slow cooker.

Combine stout beer, hot water, maple syrup, brown sugar, molasses, balsamic vinegar, Worcestershire sauce, paprika, garlic salt, pepper, mustard powder, and liquid smoke in a bowl. Mix well and pour sauce over beans, pork, and onions in the slow cooker. Add the reserved bean soaking liquid.

Cook on Low until beans are tender, about 10 hours. Drain to desired consistency before serving.