Supporting general hyperlinks starts making more sense if we have cases other than alternate (I've written elsewhere about this) because the amount of duplicated information is much greater. If you're only supporting feeds that serve as an alternate form of the content, then it makes sense to repeat one link once just to make the programmer stuck writing the user agent. I'd hope that whatever library/toolkit they're using supports XPath queries. Using them makes it easy to pluck out anything with type="application/atom+xml" and an href property.
Maybe atom needs only one link with a rel attribute, but there are others. I have a lot of hyperlinks with rel attributes on my weblog homepage, and I refuse to repeat them all as link elements.
-- Sjoerd Visscher http://w3future.com/weblog/
