That may be. But that doesn't mean the MC can't catch and use Xerneas on their team. Besides wouldn't that also be keeping the player from using certain Legendaries?
There actually is other things to base this theory on;
Like the fact Xerneas hasn't been seen in the game yet (as of V12), despite being the main Legendary of the game and even the game's icon. So, there's a possibility it may show up in version V13.
The only question is: who will use it?
I for one, would rather the MC using it, then someone else... (and it's not just because i want to use it