Just to avoid confusion, the "bottom" two engines are not the ones on the pods below the entire ship, they're the bottom two of the 6 top ones
Yes, I've played Homeworld 2. (Yeah, that was sorta what gave me the idea.) (Yeah, I'm nuts.) (I still want to see something like this tried though.) 
Me too, but I didn't notice those. Which ship is it?
I don't know the nature of the array you speak of (I'm new to FS2 modding) but couldn't you make two arrays, one for the top oval ones, and one for the bottom cricler one?
It's not a technical thing or problem, it's just a visual thing.
...In my opinion it should look like the textures...that's how V wanted it to look like.
Otherwise they would've given the Iceni rounded engines, but they prefered the oval ones. So there.
...either that or just do both...have one version with round engines and have one with oval engines...shouldn't be too much trouble...and it'd appease the masses.
IMO you're right and wrong. They could've given it 8 small circular engines plus 2 bigger circular ones on the top, that wouldn't have been a problem (except maybe they wanted to keep the number of thrusters down, to increase performance). However, they couldn't make the two bottom engines exactly the same, because they used a tile texture, and there'd be 1.5 engines on both sides, so they had to make them wider.