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I think you should first determine if Scrivener meets your specific needs for a 'word processor'. If it doesn't there is little point worrying about how it might integrate with calibre or anything else. There's a Windows wp program called Atlantis that's quite popular amongst writers - perhaps you could run it under Parallels or one of the other 'Windows on OSX' gadgets.
That said: Scrivener uses a folder structure for projects. Whilst the user can control where a project folder is located, what's inside is determined by the Scrivener software. As you know a calibre uses a folder structure for libraries. Again the user can control where a library folder is located, but what's inside is determined by the Calibre software. The content of a Scrivener project and a Calibre library are chalk and cheese.
As I see it, tools like Evernote and Onenote are good for marshalling raw materials, Scrivener, Storyist etc are the factories that transform the raw materials into a product, and Calibre is the finished goods store. As in all such things there are under and overlaps.
BR
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