They will most likely be released as Shinies in the future.
Most Legendaries have been released in their Shiny forms via events, such as the Creation Trio, the Legendary Dogs, Jirachi, Mew, Genesect, et cetera. We can only assume that Game Freak programmed Shiny sprites for the likes of Xerneas, Yveltal and Zygarde for the sake of making them available in the future.