If it bothers you that much, just shrink the components as small as you can, and design your ships in a way that fits the style you have in mind.
Here's two shots from two different in-work frigates I have.
The Terran 'Stiletto':
The Drath 'Ketaka':
The Drath ship looks a little 'busy' without being able to rotate and see the full shape of it...
Regardless, I decided that my Terran ships will use drive-systems that are more blocky, somewhat more conventional-looking. The shape of the engines on the Stiletto was inspired somewhat by the Frigates from Homeworld.
The Drath, on the other hand, use large reactor chambers. Some are more centrally-mounted instead of being so close to the thrust nozzles, but it's a prominent feature of them nonetheless.
Are you going to tell me that these look anything alike?
