there is a different quality of black to the space the ship passes through than the rest of frame in some shots as well.
A "different quality black" is usually indicative of laboratory opticals, rather than in-camera latent image photography. I can't speak with any authority on ALIEN, as I don't remember much—if anything—I might have read about the VFX work.
Sorry I'm getting back so late. I wasn't referring to garbage mattes (and if you want to see some REAL bad ones of those, 2010's are just jaw-dropping), but rather that the half of the frame the ship inhabits is lighter black space, as if it had been contaminated somewhat -- which it has. When you make multiple passes in-camera, exposures can build up and contaminate the image, which is one of the reasons why the quality of blackness is a real sticking point for me on space movies.
I'm pretty sure this is most evident on shots of the ship and refinery going away from camera towards the system. I will check my fotonovel and see if there is anything visible on that (unlikely, the pic quality there is not exactly blu-ray!)
The articles on ALIEN kept talking about tons of roto work for the ship shots, but I think that was only done for a few shots, with the rest DXed.