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@Idolse - yes you are correct in there is inconsistency between the two plugins.
The Quality Check plugin does not check the manifest, it just looks for files of that name. As you have found above the Modify ePub plugin does check the manifest. I agree they should be made consistent. I appreciate your investigation that unmanifested xpgt files have no effect, I had no idea of that. So I will change Quality Check to also check the manifest (with your extra mimetype). That way any unmanifested xpgt files will be identified in the unmanifested files check and can be removed using the remove unmanifested files option in this plugin.
The css file stuff I will keep mulling over. I confess to rarely changing body/page margins myself, as the ePubs I have edited haven't needed it. There is the standard 5pt left/right margin that Calibre puts in place, but for my own purposes that hasn't been an issue. Perhaps as a Kindle owner and Calibre's own "margin removal" option around mobi I have that taken care of elsewhere, I do not know. Far more often I see epubs where it is either the xpgt file or other non-body/page styles that have nasty large margins set on them like top/bottom or large left/right. That tends to be very bespoke to fix though of course, as you do not want to affect indented paragraphs versus whatever is impacting the whole page when a badly edited book is not as you say relying on @page.
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