Yah, it was said earlier in the thread that you can only make Pokemon hold the Red Orb only after you catch/KO Primal Kyogre/Primal Groudon(iirc)Here's something I tested that I don't think anyone here has.
(The following is written from the perspective of Alpha Sapphire)
After Team Aqua steals the Blue Orb from Mt. Pyre, you acquire the Red Orb. I know that this is the hold item you need to get Primal Groudon. So I transferred over my old Groudon from Ruby. I couldn't equip the Red Orb to it nor would it go Primal. I'm guessing it either doesn't work at all in Alpha Sapphire, only works for one spawned in Gen VI, or won't work until later.
Edit: Aargh, ninja'd by the same guy, on the same thread in less than two hours