You guys are missing the possibly obvious answer on Eden's origins...

Back in FF8, Eden was the final and ultimate Guardian Force. In Akademia the research papers mention they decided to create being made to fight back the calamity facing them, which they called Guardian Forces. Since Eden was the ultimate Guardian Force in FF8, it goes to reason that this Eden is in fact their greatest Guardian Force made right before the summoning of Zodiark. It's far more likely that Eden is able to control the forces that be simply because the Ascians in the past created it to do so, thinking they could avert their calamity that way.