SJ, you are simply a genius at modding SE4! I hope that talent pays off in the real world
To add to your idea, though, how about giving all "surface" components the Armor ability so they get hit first, thus protecting the inner components and possibly balancing the two ship styles?
Then you could also say that bigger ships a greater proportion of internals than smaller ships do, and really get fancy! Maybe you could make the different hull types separate tech areas, as well - after all, it is a different kind of engineering to hold together a spindly Excelsior class cruiser or X-wing fighter than is is to build a sturdy Borg cube or Death Star!