As I recall (I've slept a few times since then . . .), GT ship design was a modularized, somewhat-streamlined version of their basic GURPS Vehicles design system. At the time I was using GT, if you wanted to build something odd, you could simply go back to GURPS Vehicles, build whatever it was and plug it into your GT design.

The only interface issue you really needed to look out for is that GT module stats already incorporate the "slice" of fusion reactor needed to power the module, including a proportional amount of fusion power plant core. [Don't ask me how they calculated that last bit - I still suspect it as handwavium propaganda.] So you will need to calculate that for your self-built module. If you don't want to fiddle with trying to figure out how much of the fusion plant core to add in, just lump in the whole thing. That's what I did. It's not very much at all and so only really matters on very tight designs.