|Quoting 787engineer (Reply 2):|
It's the only thing big enough to carry the 787 fuselage barrel sections so that is what Boeing will have to go with no matter how unaerodynamic it is (it's faster and probably cheaper overall than shipping by boat).
Considering how expensive airplane components are, it is indeed more economical to ship by air.
The alternative involves an overhead of billions of dollars of equippment and people, continously in transit and essentially contributing nothing to overall productivity. For example, you want some sort of insurance when shipping fuselage barrels that cost several million dollars. Faster ship time means less insurance costs.