No, I believe that not everything an author writes is a political manifesto for their ideas. I believe some is, and in fiction this could be a very variable amount. The chance of minor plot or character features being such a clear representation of the author’s views is even smaller, compared to general and major plot dynamics or characteristics of main characters. Your Lovecraft example I think is very fitting, as even I (who studied few of his works) know a bunch of short stories entirely focused on the issue of “others”. It’s way more reasonable to infer the views of the author when this is a recurring theme, core to some works etc.
BTW from a logical standpoint, the negation of “everything” is not “nothing”. Me saying that I don’t think every element in a book is a manifesto doesn’t mean no element is.