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I can tell you are sceptical but Toxaris is exactly 100% right here. The content.opf inside the epub has many pieces including a manifest listing every book file and its mediatype inside the epub, a spine that tells the reader the sequences of files for reading purposes, a guide to show key locations and starting points of the text (epub2 only generally), and a metadata section where all of the metadata associated with the epub is stored. Most readers parse this file to understand how to "effectively" present the epub. Inside an epub you also have an ncx file that stores a table of contents with links (epub2), or under epub3 a nav file used for toc navigation.
When you actually change things using the metadata gui, you are actually changing information stored inside the metadata section of the content.opf file (internal one not the calibre generated local copy outside the epub).
Hope this makes things clearer.
KevinH
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