Very nice. I've fallen into the same trap a time or two, in mixing up my mythology and history of my game's setting. It doesn't help that I'm largely disorganized, and a good portion is scattered amongst multiple files and some mixed in with the mechanics.

So the only thing I can add is to keep well organized, which will help keep your mythology and history separate, as well as make it far easier to reference things later.

Interesting article.

This reminds me of my old pen/paper RPG days. In the campaign we played, history starts to blend into mythology as you go farther back in time (much like Tolkien's history). Much of the adventuring revolved around sorting out the true history from the recorded mythology. Of course, in an RPG, much of what people consider mythological elements (gods/magic/heroes) may be present, but over time the actions of these said entities become twisted into morality plays (or metaphors, as your article points out).