The Strange Souvenir Hiker is in XY, so SM was definitely planned way in advance. With that in mind, I don't see why they couldn't have planned for Zygarde to be of importance in SM, too. The red and blue on Zygarde Complete already correspond to Xerneas and Yveltal; and while light blue could go along with Xerneas to an extent, I can't see how orange would relate to the red-and-black Yveltal, so I'd say there's a chance the light blue and orange go along with Lunala and Solgaleo instead.
Also, I don't think they're gonna make a "definitive edition" for SM when they're supposed to be the "big anniversary titles," meaning probably no third version to go with them. So I'd honestly rather there not be a third member to their trio and instead see them do something new and connect the gen 6 and 7 legends via Zygarde. It could definitely turn out interesting and unique if done correctly.