I like how there's all this "It's not a prequel to Alien" tripe, and then EVERY ELEMENT of the film revealed so far refers back to Alien.
Horror both psychological and ichy? Check
Strong female lead(s)? Check
Weyland (Yutani) Corp.? Check
Android crew member? Check
Space Jockey? Check
Alien Egg-type things? Check
Melting helmet faceplate? Check
Med-bay patient shenanigans? Check
Direct threat to mankind if it gets back to Earth? Check
Ancient Alien Reference? Wait, you mean like in AVP? Check
It takes place before the events of Alien. It involves concepts, artifacts and beings that will, in universe, appear in some form in Alien and elsewhere in the franchise.
It is a prequel to Alien.
Other movies have also taken place in universe before Alien, and like the dreaded Star Wars prequels, still exist in the real world. Get over it.
EDIT: Forgot to mention...Trailer Music & title reveal for new movie matching the original film? Check
I think the idea is not that it isn't a prequel to Alien. More that, if Scott's claims are true, it doesn't necessarily lead in to Alien. In other words, it would effectively be a reboot, starting with the same or similar characters and certain locations from Alien's backstory. But if another film is made it would diverge from a timeline that includes the original alien.
And honestly, I would find that quite interesting. For example: nobody doubts the quality of Cameron's Aliens. But Cameron did invent things Scott never intended originally. By making the xenomorphs "animals" complete with a queen, Cameron overwrote Scott's original, potential concept of the xenomorphs as purely biomech tools and war machines deployed by the civilization of the crashed ship.
Scott may have decided to get things "back on track" by just starting from scratch and portraying the alien technology, and any biomechanical creatures spawned from it, inline with his original concepts. Further films in a Prometheus timeline could go very different places than the Alien franchise had before. For example, war between humanity and the true alien civilization itself, in which creatures such as the xenomorphs are merely devices and not the stars of the show.