Word count is supposed to be just the story text, not any copyright, series listings, other books, blurb, about the author, reviews, publishing history, contents list, headers or footer.
It may include the words "The End" if the book has them. Chapter titles, chapter preambles etc would be included, if they exist.
I'm not sure about notes, preface and an appendix.
A prologue is really chapter 1 by another name and epilogue the last chapter, so they are counted. We recommend against using those terms for the story before the main story and the story after the main story as it seems some people confuse preface and prologue and many think both can be skipped.
I do think a preface can be skipped and if added by the publisher to a later edition should always be read after the book as it's likely to have 3rd party opinion and spoilers.
LOTR is an example of a book where the notes / appendix maybe should be counted?
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