The Comets were brand-new technology, they were designed with unanticipated stress points in the skin that didn't react well to pressurization, and once they were analyzed, the problem was fixed. Too many people had been killed, thought, and the Comet never made it back. It was only in service for 10 years or so.
The DC-3 has been flying for 85 years now, the B-52 for 65 years, and the wing flexion is designed to work that way. I don't have a problem believing that any fatigue factors have been fully proven out and figured into the calculation ....