Remove the short ribs from the fridge about an hour before cooking, if possible. It won't greatly affect the outcome of the dish but helps in the searing process. You can trim some of the fat if you like. Season all sides with salt and pepper.
In a dutch oven or large heavy bottom pot, heat 2 tablespoons canola oil over medium-high heat. When the oil shimmers, sear the short ribs about 3 to 4 minutes each side until browned. Transfer the seared ribs to a plate.
In the oil and rendered fat, sauté the onions, garlic, and peppers for about 3 to 5 minutes or until the onions are translucent and the garlic is fragrant. The vegetables will continue to cook as the chili simmers.
Pour the beer - or 1 cup stock if substituting - into the pan and gently scrape any bits of short rib that stuck to the pan during searing.
Add the remaining ingredients to the pan: chipotle peppers, chipotle peppers sauce (optional), tomatoes, tomato paste, kidney beans, black beans, pinto beans, chili powder, cumin, marjoram, cayenne, white pepper, cocoa powder, the short ribs and any juices that collected on the plate. Stir until combined and reduce the heat to low. Cover and simmer for 2 ½ to 3 hours or until the short rib meat is easily pulled apart with a fork.
Stir the chili occasionally. The tomatoes will break down as the chili cooks. After cooking, transfer the short ribs to a plate. Using two forks, shred the meat as chunky or fine as you like. Return to the pot and stir to combine.
Enjoy immediately or to lighten up the richness, chill completely in the fridge and scoop off any fat that solidifies before reheating.