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I'm afraid I have zero interest in the EPUB spec. So I have no idea what version of EPUB calibre produces. All I can say is that calibre produces files with the following two goals in mind:
1) Work on the widest variety of devices possible
2) Render as close to the input document as possible within the constraints of (1) and the user's conversion settings.
The EPUB spec(s) are largely irrelevant to both those goals.
That said the OPF inside the epub that calibre produces uses package version 2 which is the same as that used by the EPUB 2 spec.
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