Season short ribs with salt and black pepper.
Whisk gochujang, soy sauce, honey, vinegar, garlic, and ginger in a medium bowl.
Heat oil in a large pot over medium-high heat.
Working in batches, cook short ribs until well browned, about 5 minutes per side.
Transfer ribs to a platter as they’re done.
Add onions to pot and cook, stirring occasionally, until golden brown, about 8 minutes.
Add gochujang mixture to pot and cook, stirring often, until darkened in color and bubbling, about 4 minutes.
Add chicken broth, beef broth, and chiles.
Return short ribs to pot, bone side up, along with any accumulated juices.
Cover pot and bring liquid to a simmer.
Reduce heat to low and gently simmer, partially covered, until meat is very tender but not falling off the bone, 2½–3½ hours.
Uncover pot and increase heat to medium.
Continue to simmer until sauce is thick enough to coat a spoon, 10–15 minutes (it will be slightly thicker when it cools).
Serve short ribs over rice, topped with scallions.
