The epubcheck developers recommend to declare a fallback as follows:
Code:
<item id="css" href="epub_css_r1.css" media-type="text/css" />
<item id="xpgt" href="page-template.xpgt" media-type="application/vnd.adobe-page-template+xml" fallback="css"/>
Unfortunately, this method doesn't work with epubcheck 3.0.1 and has been officially recognized as a high priority bug:
Non-core media type stylesheet check ignores fallbacks (ePub Check 3.0.1) #271
Hopefully, this bug will be fixed in the next version.