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@iaetheia - there seems to be multiple things you are throwing into the mix here. These are the facts:
(1) The calibre ebook viewer will display from the very start of the book (be it epub or whatever other format like mobi it converted to epub to display it). So if the first page in that book is a cover image, that will get displayed.
(2) Mobi formats on a Kindle device do not display the cover image when you first open the book. It intentionally skips past such covers, as Amazon ideally want the user to be able to start reading straight away. Some people fudge this using duplication (so a content page following the official cover page and duplicates the cover image). But that is a silly thing to do in my opinion in that it bloats the book and you can't easily replace the "inner" cover. As dwanthny said initially, if you want to see the cover on a Kindle device just click the left button after opening the book.
(3) Both of those facts bear absolutely no relation to what this plugin does. Calibre stores in its library folders for each book a cover.jpg file for display on the book details panel. This plugin modifies that jpg only, nothing else. As does drag/dropping an image onto that cover in the book details or edit metadata window. As does downloading a cover using metadata download. As does using the "extract cover from ebook" feature. Not one of those approaches will change the cover inside the book itself in isolation.
(4) If you then want that cover.jpg which you have sourced/generated to be *inside* your book (so it can be displayed in the calibre ebook viewer or on your device), then the post above from dwanthny lists all of your options for making that happen.
Hope that clears things up for you...
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