I don't think they were meant to be different, as the narrative does imply it's them and so do the post-release interviews.
That said, I don't buy the whole 'budget' excuse either. We must be living in the worst financial crisis in human history if a 100,000,000$ film can't afford make-up and wardrobe for its extras.
They didn't even get the scale right. You know how, when they wanted to preserve the correct scale of the set in Alien but couldn't, due to budget, they used kids? And you know how when they wanted to fully recreate the space jockey room for the film but couldn't, due to budget, they made a quarter of it and made it rotate to create the illusion of a full thing? This film doesn't even attempt at hiding the so called "budget issues". Even the scale of the engineers is off. They're all the size of regular humans.