Why not have a central body type, that you could just "assemble" into the other shapes?
Im sure your could find a shape that is included in the bodies that you want to change to. Basically a main piece, fully functional on its own, with attachments that could make it into a Strat, Tele, or whatever else.
In example, you could take a Rhodes V and turn it into an Ibanez Xiphos with a few attachment pieces.
I had this idea awhile back too, except that the main shape of the "Hub" guitar would have tone dials/Pick up Selector/anything else in the general places where they would be on any guitar, and then you take parts/additions and build off that. Im sure someone could devise a system of snaps, locks, even pegs that would work.
Hell, I might try this sometime.