Well the theory is that Deoxys itself was created by the beam of the weapon, not that itself was involved in the creation of the weapon. It makes sense when you look at it's dex entries (which GF may have had in mind when making XY). GF tend to develop the remakes alongside the third versions (FrLg's close release date to Emerald's in Japanis a sign of that...I wonder if FrLg weren't released so close to Emerald than they might have done better, and GF mentioned how they developed Pt and HgSs simultaneously) too so they may be using OrAs as a steping stone for what's next. Actually the Mega Latis and Mega Blaziken seem to further hint that GF had in mind. I once read a rumor that GF think up what the next generation will be during the previous (for example Gen II during Gen I, Gen III during Gen II, and so on.)
Btw do you think they'll add some new story elements to MM, they did say they wanted to make it more than just a remake.