In the last maneuvering thrusters build, I added a variable to subsystems in Lua: Position. This should let you do subobject translation, with clever scripting.
The limitations are that due to how FS2 culls graphics, if the ship goes out of view, so will the subsystem (no matter where it is).
Also, collisions will probably not work properly and be unreliable.
Finally, that variable edits the model data stored in memory. So, if you move a subobject, it will move it for ALL ships using that model, and it will not be reset between missions.
So it has very limited usefulness, but I figured I would mention that if anyone wants to play with it.