Ah, didnt realise what you meant.
But you can (for example) trade a Groudon into Ruby, and battle the Groudon in it with it.
Doesnt cause the game to melt, or rip a hole in the space/time continuem.
I do see your point, but the player can (Theoretically) have 6 of the same legend. So why not the champion?
It could be that once you beat the champ, the Legend is released in the after story for you to catch, meaning you cant have it at the same time.
Just thinking.