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Assuming that the original AZW3 had a cover the EPUB conversion will also have an internal cover. The cover.jpg you see is a copy of that cover converted to JPEG. The metadata.dat file is also a copy of the metadata in the file. When viewing folder inside of Calibre's library you may be seeing a cover.jpg and/or metadata.dat file that contains data newer that that actually in the book if either the cover or metadata has been changed after importing or converting the book.
Calibre never displays the book's embedded cover. Doing so would be a nightmare. It makes a copy of that cover when the book is imported and saves the copy in JPEG format regardless of the embedded cover's format. That way Calibre can display the covers quickly and do so without having to conversion formats in realtime. By default, it also saves the external copies along with the book itself when using Save to Disk, though this can be changed in Preferences.
"Teaching" Windows Explorer to read the book's internal cover is outside of Calibre's domain. Extensions can be created for Explorer to give it additional skills like this, but Calibre doesn't provide one.
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