First, there's already a configuration file for both the passenger and the cargo version in the sharing section here, which you can download without having to customize the airplane yourself.
And, you should't take the diagram in the GSX configuration page literally. The main cargobay doesn't *have* to be between door 1L and 2L, the only thing that matters are the coordinates of the door so, in case of the 747, the door can be configured in its proper location, behind the wings.