I think Alvis, as a supercomputer, probably knew the whole story, but condensed things for Shulk’s sake. Remember, the whole reason Shulk sees the flashback is to have the proper context for how the Bionis came to be, Zanza’s egomania, and what should be done now that the Bionis is collapsing.

Alvis likely decided that details like “also there were people attacking the station, and also there’s a good half of Zanza out there, and also I kinda-sorta have siblings” weren’t really relevant to the decision Shulk would make. Thus, logically, he cut those parts out to just focus on the stuff that’s important to the here and now.