if you were building a sci-fi system that highly integrated ship board operations with game play, you might have to include class features for a given PC class that accomodates such mechanics - thus needing to revamp every PC class that might be a ship's officer to include such aspects (a lot of work).
Well, I'm thinking that the features are not really that tightly integrated. Typically, in the fiction, the skills and abilities used "away" and those used in starship combat are fairly disjoint. So, the systems can be largely disjoint. Then, with one system, you have the choice - if you don't care much about ship combat (like, say, Firefly), then you largely ignore the subsystem. This won't tend to be unbalancing, so long as you make sure most character choices include the options.
If you are playing with class and levels, then various classes give starship powers or feats in addition to whatever else you'd get. If you are skill based, then at skill levels X, Y, and Z, you get powers or feats, again, in addition to whatever the skills do outside combat.
Adding in fighters then becomes pretty simple - one of your combat roles is "fighter pilot", which you can scale from individual to group leader fairly easily, I suspect.