I've noticed several virtues and flaws that is listed in several categories. Like Visions, for example. It's both a Minor Story Flaw and a Minor Supernatural Flaw. Pagan is both Major Story Flaw and Major Supernatural.
Does this mean that the flaws are both categories at once, or can you choose which category to use it for? I can't remember reading anything specific about that?
I would say its a matter of SG discretion. If you want it as a seed for your own storytelling then make your player take it as a Story Flaw. If you don't want to have to bend your mind around incorporating it as a praticular element of any part of the story, then get him/her to take it as a Supernatural Flaw.
Don't think any special rules need be dug up on this matter.
In my group, we deal with the issue this way, as it concerns the limits of how many virtues/flaws of one kind you may have. I.e. in most cases, you may safely bend the limits, as long as the Virtue/Flaw is of an hybrid type. It adds flexibility of character concepts.