Not neccesarily, then again it depends on your description of the word fan fiction. Did kishi directly confirm or deny any of the assumptions we have made? Ofcourse not. Are we fans? Yes. Is Naruto a fictional manga? Yes. So yes it is all Fan Fiction. But I dont know how that adds or takes away from anything that was said.
Let me put it in a simpler way. If you walk into your house and hear barking, look on the floor and see dog poop, and see a flyer for a 50$ puppy laying on your counter. The first thing you would assume is someone in the house just bought a puppy. Now you CANT state this to be a fact because you just dont know, there is a just that this is all an elaborate plot. But CHANCES are that someone did buy a puppy, and you shouldnt be faulted for acting upon that assumption.
That is what Theories are, there are assumptions created through hints and evidences found within the Manga and although the manga does not DIRECTLY say said assumption is true or false through common sense we can all agree that it is likely to be so.
Lastly I want to tell you that when you look at a Theory you should not be judging whether it is true or false or right and wrong. But rather whether or not it is likely or unlikely. And if it is likely then how likely is it, somethings like jiraiya being dead is highly likely while things like Jiraiya being Tobiramas son is highly unlikely.
Also remember that there is no such thing as a factual theory, rather a factual theory would fall under the category of an explanation or a statement but not a theory. A theory is a speculation, and you cannot speculate about things that are facts.
I hope that helps answer your statement x__x
