This is one of those silly questions that's been bugging me for a while. Have you ever checked a site's backlinks, and found that many of the backlinks Google reports are from the same site? How does this work? Does it actually help rankings?
I don't believe the link operator was designed to just show backlinks. It was designed to show links (from any source) pointing to the URL you used with the site operator.
That makes sense on one level, but if that's the case it's very inconsistent. Just about every site has links throughout its pages back to it's home page. Yet site:url doesn't show self-backlinks for many sites (like mine, for example).
From what I've seen, sites that use relative URLS for internal linking are not as likely to see themselves listed in the link: operator as sites that use absolute URLS for internal linking. I really doubt it has any impact on rankings though.