Most URIs in the head are relative, but feed URIs are fully-qualified. It is unclear why this is the case. If they were relative, the feed hrefs would take up less space in the output.
The relevant code is in OutputPage.php
$tags = $this->feedLink(
'rss', $rctitle->getFullURL( 'feed=rss' ), wfMsg( 'site-rss-feed', $wgSitename ) );
Changing this to use getLocalURL appears to work.
(There's a similar issue with the UniversalEditButton extension. I understand this is to be integrated into 1.14.0; if so, this code may also need modification.)