if the director wanted the Alien to be attracted to the flares then he would have made the flares brighter and the environment darker in comparison.
And then the prisoners would be unable to see.
But it's not like that particular director got his way on that film, even complaining about the lighting: “I could not get the screen to be black, I couldn’t get the creature to come out of the shadows unseen.”
But it's beginning to become moot: C.A. seem more definitively inspired by the unused scene from Alien than an interesting but inconsequential thing from the third movie.