Well, yeah, I see what you say, but as I understand it any part of the model within the subsystem cube will be part of the subsystem and take damage to that subsystem if hit. If that makes sense.
What I wanted was to be able to define, say, a really long thin piece of my ship as a subsys. Case in point - the bridge of my carrier. Now, the centre of the subsys cube needs to be roughly in the centre of the bridge bit of the model, or the aim cue will appear in a funny place. If the cube I define is too big, parts of the hull are incorporated in to the subsys. But in avoiding this, the susbsys isn't wide enough to take on the whole bridge superstructure - the edges aren't included in the subsytem. If I could define a cuboid, I could make a subsys box wide enough to include the width of the bridge, without having to be equally tall and thus 'clipping' parts of the hull I don't want it to.
