I think a large part of this lead comes from the way the engineering responsibility is distributed (at least for the R&D side), where the engineers responsible

I think a large part of this lead comes from the way the engineering responsibility is distributed (at least for the R&D side), where the engineers responsible for certain parts are in the internal tracking system so that engineers responsible for other parts can just look them up and work with them directly about changes they could make to their parts to improve things for the other part. I think most other organizations have a lot more bureaucracy involved in making changes, which makes them slower and more expensive. Plus, SpaceX doesn't try to spread out its operations across the US to act like a jobs program, while the other big space contractors have advertised their presence in every state as a reason they should be picked, which obviously increases costs.