In a medium saucepan, melt the butter. Add the onion and cook over moderate heat until softened, about 5 minutes. Add the garlic and cook until fragrant, about 1 minute. Stir in the ketchup, bourbon, vinegars, molasses, honey, chipotle, thyme and cayenne. Taste; if you like more heat and smoky flavor, add reserved adobo sauce. Simmer over low heat, until thickened, about 40 minutes.
Transfer the barbecue sauce to a blender or use immersion blender and puree until smooth. Season to taste with salt and pepper.