You are all wrong a bit.
5/6 years ago Scott had plans for a sequel already dealing with the SJ, he talked to James Cameron about that and both agreed that Fox needed to stop using the franchise and let them start working on the project.
Fox did not listened and continued the AVP nonsense.
When AVP requiem critically bombed (i think it mades its money back even earned some) FOX knew that they had to do something to keep the cash cow alive and recontacted Scott about doing another ALIEN movie.
He said ok this will be a prequel and i'm not directing it but my stepson Carl Rincsh will.
Fox refused Scott protegee asking him to direct the movie.
Scott said ok, his idea was for 2 R rated movies that were real prequels leading to the events of ALIEN.
Jon Spaihts wrote that direct prequel, wich was going to be cut in 2 movies (wich included the proto alien, the derelict landing on LV426 and the special Order 937 sent to mother).
Scott asked for a budget of 200 millions dollars, FOX refused, no way they were going to put that money in 2 R rated movies especially for a franchise thats almost dead in the water.
Then Scott had the idea to sell the movie as a new franchise.
Asked Damon Lindelof to remove/merge some scenes and transform all the direct links to ALIEN in order to make the story work as one movie cutting the budget in half.
Scott also asked to have the liberty to shoot an R rated movie but agreed to deliver also a PG13 cut.