Now that Fassbender has basically confirmed that yes this is connected to alien I think we can safely relax a little.
From slashfilm.com -
Fassbender (when asked if it is an alien movie and if it follows the continuity with the alien movies) -
“Oh, absolutely. There’s a definite connecting vein,. You realize you’re part of something else, but it’s definitely in keeping with the old ones.” … “When I read it, I was like, ‘Well, okay, another Alien. Where do you go with this idea?’ And then I sort of read the script, and it’s new, yet it’s in keeping with the old traditions as well. But there’s a whole new revelation within this film.” …. “The first ‘Alien’ [movies], they were thrillers. Something’s going on. It’s creeping, it’s sinister. Things are happening, it’s building, [and there are] different sorts of intrigues and politics going on between the different relationships on board. There’s action in it,” he said, “but the intelligence is what struck me when I read it. It’s more sort of like the original ones. There are things happening and building, and the intelligence of the first two-thirds of the film gets you ready for the action.”