Whisk olive oil, lime juice, lime zest, garlic, cumin, red pepper flakes, and chipotle pepper together in a large glass or ceramic bowl. Add sirloin and toss to evenly coat. Cover the bowl with plastic wrap and marinate in the refrigerator, 30 minutes to 2 hours. Preheat an outdoor grill for medium-high heat and lightly oil the grate. Remove sirloin from marinade and discard marinade. Thread sirloin, red bell pepper, green bell pepper, and onion onto skewers. Cook on the preheated grill until sirloin is browned and vegetables are tender, about 4 minutes per side.