With Steven still being Champion, they are saying that Ruby/Sapphire's story takes precedence over Emerald's.
Well, D/P and Platinum also have conflicting stories... stories of Giratina and Cyrus are different in those games. If they've chosen Crystal's and Platinum's stories to be canon, they will also choose Emerald.
They will never exclude any third game from canon. Emerald is also part of canon. We just don't have proof yet, because R/S/E seem to be last in timeline. Platnium is already proven to be canon only because it takes place before B/W and B2/W2.
Assuming that all third games are canon, World Tournament confirms that B2/W2 take place before R/S/E.