Add the drained, soaked beans directly to the Dutch oven with the softened aromatics. Pour in the molasses, ketchup, apple cider vinegar, yellow mustard, nutritional yeast, smoked paprika, chipotle powder (if using), soy sauce, brown sugar, black pepper, and 1 tsp kosher salt. Stir to combine, making sure the molasses is fully incorporated — it tends to sink and pool at the bottom.
1/2 cup blackstrap molasses, 1/4 cup ketchup, 3 tbsp apple cider vinegar, 2 tbsp yellow mustard, 2 tbsp nutritional yeast, 2 tbsp smoked paprika, 1 tsp chipotle powder, 1 tbsp soy sauce, 1 tbsp brown sugar, 1 tsp black pepper, 1 tsp kosher salt