Yes, in EPUB, calibre will use the first page of the manuscript in preference to the <guide> element (this is in accordance with the EPUB spec), unless for some reason the first page cannot be rendered.
If you want to force the use of a raster image, add the following to your EPUB:
<meta name="cover" content="id of cover image in manifest"/>
inside the <metadata> element.
And if you want your EPUB to work across all EPUB readers, you should ideally insert a simple HTML file as the first item in the spine that includes your cover image.
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