To be a bit more succinct than my previous reply, I think there is a legitimate distinction between "making up content to fill up spaces not covered in the original story" (i.e. fan fiction) and "reasoning out as much as you reliably can about what filled up those spaces, and no more".
Fan fiction is creative writing, more or less by definition: inventing new details is fine unless they conflict with the original story (or even if they do). The author of this article is very explicitly trying to avoid "making up" an answer: he's searching for evidence only within the original story that could constrain the answer to a question relevant to that story. They're both games for fans to play, but at least to my eye the two are worlds apart.
Except the evidence in the original story is clearly insufficient, and absence of evidence is not evidence of absence. We know nothing of Sauron's capabilities to detect and confront airborne intrusion into Mordor or about Gandalf's assessment of these capabilities. Assuming Sauron could not see or bring down the eagles and that Gandalf was aware of this fact is, from this point of view, adding new elements to the story and therefore fan fiction.
Fan fiction is creative writing, more or less by definition: inventing new details is fine unless they conflict with the original story (or even if they do). The author of this article is very explicitly trying to avoid "making up" an answer: he's searching for evidence only within the original story that could constrain the answer to a question relevant to that story. They're both games for fans to play, but at least to my eye the two are worlds apart.