I can't speak for what they are trying to say but my thoughts on Zelda lore is that Nintendo goes with the approach that myths, stories, and religions change over time. Like in the real, there was no set canon for Greek or Roman mythology across hundreds of years. Sure some major details persisted by details change over time. Modern day Christian beliefs and practices are significantly different than the earliest Christians. The core idea that Jesus was the son of God wasn't even a concept for many early Christian groups.
In that same manner, the Zelda mythology changes over time. In each game, we are only seeing a snapshot of that time periods particular mythos. In some games, the three goddesses and the Triforce are the main symbols of Hyrule religion. In others, they are barely mentioned and it's Hylia that is the main focus of worship. What the players know as canon may not be what the characters in game know as canon because they weren't there to experience those events. They only know about past events from storied passed down over generations. A vague memory of something that happened long ago.
In many fictional worlds, the lore and mythos are firmly established by the creators and they make sure all events and facts fit together neatly. But the Zelda series isn't concerned about that. You get some loose connections and details that appear wrong. But that's because the mythos is told through the viewpoint of the people living in that specific period of Hyrule. The past can never be 100% knowable. It conveniently allows the Zelda team to change details as needed without needing to adhere to a strict lore Bible. But to me, it helps make the world much grander and unknowable.