Add the onion and cook, stirring often, until soft, about 3 minutes. Add the chiles, garlic, ginger, thyme, allspice, and nutmeg; stir until fragrant, about 1 minute. Add the marmalade and stir until melted. Fit the insert into the slow cooker. (If using a skillet, scrape its contents into a 5- to 6-quart slow cooker.)
Stir in the broth and soy sauce. Nestle the short ribs into the sauce, pouring any juice from the bowl on top. Cover and cook until fork-tender, 5 to 6 hours on high or 9 hours on low. (The short ribs can stay on the keep-warm setting for up to 2 hours.)
Use tongs to transfer the short ribs to serving bowls or a platter. Strain the sauce into a fat separator; set aside for a few minutes. Pour the defatted sauce into a 3-quart saucepan, add the vinegar, and bring to a boil over high heat, stirring occasionally, until reduced by half, about 8 minutes. Stir in the basil and cook for 1 minute to let the flavors meld. Season to taste with salt and pepper, pour the sauce over the short ribs, garnish with small basil leaves, if using, and serve.