You can’t generally embed web resources in EPUBs; only audio
and video resources can live outside the container. Referencing a web page that
has a video in it is not compliant with the specifications, so trying to mangle
media types to get around epubcheck isn’t recommended. You might find some
reading systems that will render the content despite the restriction, but if you
do hack at the package file don’t do it with the expectation of universal
support (I know iBooks will block your content, for example).
Not sure how much luck you’ll have with flash video in epub 3
reading systems, though. A webm version of that video is available if you go to
the youtube HTML5 trial, but I haven’t heard of an easy means of getting the
URLs to those videos. You’ll have to root around in the javascript and see what
you can come up with.
Matt