Yeah, when the whole thing is done I'll mention the different ways that you can still play total god (besides creating the actual world itself) such as weather patterns, disease, disaster, etc.
As for something like the Aurora, that won't be mentioned because it hasn't had any real impact on any civilizations (that I know of) nor would I think that would even matter. You could have an entire civilization based around the aurora and it would still follow most of the patterns in this guide because it's a CIVILIZATION, that it may be based on doesn't matter. Put a piece of copper on a wooden block or a marble one doesn't matter, it's still a piece of copper. Also, the SCIENCE behind weather and other phenomenon will not be covered because that is not what this guide is about.
Now for something like Pandora with the whole floating island concept, if you read the intro paragraph it will state that the guide is operating in a world setting similar to Earth's. If you decide to add other concepts that are not "normal" for our world, then you have to think for yourself how that would change the sequence of events in the world YOU are creating. Whether or not it would cause technologic or some other kind of innovation, if it would affect war/tactics, trade, and/or culture, the list could go on and on. If you have something that you're not quite sure about then you could ask me and I'll help you out, though I would hope that you (and most people) would go and figure that on your own

This is not done yet, obviously indicated by the table of contents, and when I feel that the final version is done then I'll update the document myself as a deviation, there will not be an entirely new "How to Make a World". Or maybe I'll just alter this over time and when it's done I'll just copy-paste-delete this deviation-smack it onto a new one. It should be complete between January and March of 2012 depending if time would allow me. Even then for some time I'll ask other users to help edit it some more and make certain things better before finally submitting it to groups such as #ArtistsHospital