This is a pretty standard 3D modelling strategy, unsurprisingly, called "box modelling". You can create an incredible amount of things with box modelling. Including, obviously, a lot of spaceships. I built several crud spaceship designs with box modelling back in school. The main key advantage, is all of your 'parts' are built off of a single object in the editor, and aligned perfectly.
The other thing though, you can do to a box modelled project, is round all the edges to varying degrees, and end up with something looking much more fluid and amorphous. However, I suspect the results would be far more unpredictable if he through something like that into this script, so it'd be difficult to go there procedurally.
Yeah back when I made 3D models of star trek spaceships (trekkie in your name significant?) that was one of the go-to methods for making the shuttles, smaller craft, borg (obviously), but stuff like Voyager and the Enterprise-E you would often resort to more advanced lofting/spline patch based techniques and work off of a sketch.
I used to enjoy making 3d spaceships in Blender3d and such. Simple extrusion and resizing of faces is the path of least resistance but it doesn't lead to very nice results.
The mesh should follow the shape you wish to create, not have the shape be dictated by the geometry of the mesh.
The other thing though, you can do to a box modelled project, is round all the edges to varying degrees, and end up with something looking much more fluid and amorphous. However, I suspect the results would be far more unpredictable if he through something like that into this script, so it'd be difficult to go there procedurally.