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Cool, that was about what I discovered too. I've passed an updated Quality Check over to kiwidude, I imagine it should go up relatively soon as long as he's happy with the changes.
The check compares all css - both css files and inline style tags against Calibre's preferences. The check is relaxed when checking inline styles, as Calibre only puts the top and bottom margins in @page and left and right go to the class assigned to body. Basically it only flags an inline margin as disagreeing with Calibre if something exceeds Calibre's prefs - if the in-line margins are less than Calibre's prefs it leaves them alone.
It also ignores titlepage.xhtml - I'll make this more robust at some later point and have it ignore anything marked explicitly as a cover in the manifest.
There's also a bug in modify ePub's margin rewrites, I'll be updating that shortly.
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