Magic is science that we just don't understand yet,
Look, I get that the cool thing to do these days is to shove science into fantasy and justify it with Arthur C. Clarke quotes, but I disagree. No amount of stretching of the imagination could convince me that three powerful aliens would willingly transform themselves into golden triangles, tuck themselves away in a "Sacred Realm", all for the purpose of doing this for whoever finds them:
Good/evil heart detecting, wish-granting tech. Right.
This is the way the series seems to be going, a mix of sci-fi and fantasy.
A mix is fine. I'm excited at the prospect of Link's "book" actually being some kind of smart device, and the villains of Zelda NX being an alien race. But if
all of the Zelda series' magic was just science the Hyruleans didn't understand, it would just be science-fiction, and I like to think there's a difference. I'm not the only one feels this way about "explaining away" magic, either; just look at how many people were upset (and are still upset) when it looked as though George Lucas was using Midichlorians to give the Force a scientific explanation.
So...what if that Book turned Link into Zelda and vice-versa?
That could be cool.