I kinda like where OP’s head is at, but
>>42480329 has been confirmed in interviews. Apparently the idea is that when the wolf legendaries were fleetingly witnessed by travelers, all that most people could glimpse where indistinct blurs of color, sort of how we only have grainy and vague images of what people claim to be Bigfoot or the Loch Ness monster. Eventually, within the lore of the games people went from referring to them by their colors as “The Cyan” and “The Magenta” to just abbreviating those words into “Zacian” and “Zamazenta,” and the original origins were forgotten.
It’s kinda neat that at least some of GameFreak’s creature design isn’t just limited to referencing or parodying cryptids, but also to recreating some of the conditions/situations by which legends are originally conceived and evolve with time. Small detail, but adds a lot of depth lore-wise in games with shorter/rushed story campaigns.