Pilots can do that because they go through a ton of training and they deliberately do things to maintain their manual flying skills, including regularly taking manual control outside emergencies when the autopilot could fly perfectly well. And when a pilot takes control "for practice" there's no reduction in productivity for the airline compared to if the pilot is sitting in the seat with the autopilot engaged.
How can software engineers maintain a healthy "manual programming" skill set? What employer would be willing to pay for so much wasted time for their software engineers to do deliberate training courses, or willing to accept the productivity loss from their engineers occasionally working manually for practice, when working manually is so much slower?