On bending the facts to fit theories:
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Are you crazy?! You can't call something an error just because you want to! If you're going to doubt this one thing for the reasons you gave, then heck, why not go and doubt everything? Why not reject any piece of evidence that contradicts your personal theories, for the reason that it must be a mistake? You're bending the evidence man! That's a strict no-no! 

For example, I think I'll start believing that there is no such thing as magic in Hyrule. The ancients didn't understand some stuff, so they probably just invented magic. So, anytime we see magic being used in a Zelda game, it must just be an invention. Maybe "magic" is just a metaphor for powerful actions. Likewise, I think I'll stop believing that there is such thing as the golden goddesses and the Triforce in Hyrule. The ancients felt the need to invent some kind of watching presence, so they invented the creation myth. So, anytime we see golden goddesses and the Triforce, we are really just seeing human inventions. The Triforce is probably just a golden triangle, a lucky charm, that people superstitiously thought was granting their wishes. 

Can you see where I'm going with this? I'm ruining the Zelda universe by introducing my own theories, and BENDING the facts to fit them. The canon materials DEFINE the Zelda universe, and it is sacrilege to try to bend them to fit your own theories.

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Well, I wouldn't label this kind of theorizing "fanfic." Not all fanfic is contradictory to the canon. Strictly speaking, fanfic simply elaborates on elements that were not mentioned in the canon. It doesn't necessarily try to contradict what is told in the canon.

Rather, I would call it "arguing toward a predetermined theory." There is a famous quote by Sherlock Holmes: "It is a capital mistake to theorize before one has data. Insensibly one begins to twist facts to suit theories." This is especially true in Zelda. I see it happening all the time, even with me sometimes.

What we ought to do is, examine all the relevant facts, and then formulate a theory that seems to explain all of them (or as many as possible). Instead, many times I see theories thrown out with little thought given to the evidence. When contradictory evidence is presented, the theorizer comes up with ad hoc theories that try to twist the facts to fit his theory.

It really boils down to this: you have to play the games for yourself, and see what impression they give you. Only then can you really start to theorize. Theorizing without playing the games in question leads to messed up theories. In my opinion, you really can't talk about a game until you've played it yourself.