Thanks for the explanation, Elliot. I much prefer having the ability to add different size ship images without worrying about scaling. It's a great feature, just a shame about this side-effect.
Lordxorn, I think you can make the colour almost completely transparent, so much so, that you'll hardly notice the stars fading behind it. You're right though, the damage effect will look odd, maybe it'll be like debris floating around the ship?
I don't think there's a way to scale the Borg cube to look bigger. Looks like the Distant Worlds Galaxy will be free from fear of assimilation, at least for the time being.
I'm not sure if the game can properly depict the Borg yet anyway as a race of cyborgs who don't colonise or trade or involve themselves with diplomacy.
So I'm content to wait until there's some kind of mod feature for creating massive ships. Like I said in an above post, there must be some races that are larger physically than humans, so would need more head room in there ships, hence bigger ship's hulls. It's on the modders wishlist anyway.