Nothing. It`s the same release as found in the Dec. 2003 Alien Quadrilogy, with the first 2 discs of the boxset being the 2-disc SE coming out tomorrow. The remainding three films, and their discs, will also be released in the coming weeks - so only Disc 9 of the Quadrilogy will remain exclusive to the boxset.
HTH :)
My DVD Collection
Yes but that Alien disc in the Quadrilogy has Ridley Scott`s extended cut of the movie and the original theatrical version which the Alien Legacy Box set didnt have I believe! :/ 
My DVD Collection :D
True - how is that relevant? :/
My DVD Collection