We need at least some kind of a configurable override to allow specifying the base URL in GlobalCssJsHooks::makeCentralLink. For ShoutWiki, I literally commented out the original WikiMap code and replaced it with this filthy hack:
return '<a class="external" href="http://www.shoutwiki.com/wiki/' . htmlspecialchars( $title->getPrefixedText(), ENT_QUOTES ) . '">' . htmlspecialchars( $message, ENT_QUOTES ) . '</a>';
Needless to say that this isn't exactly a scalable solution and it makes upgrading the extension harder, too.