Links generated by LinkUtil.createLink(node) should end up with the same link pattern always. It would not matter if the link is to a root page or a child one. Links should respect the pattern defined at /server@defaultExtension.
For example, in Demopublic. You can see that generated link to root page in the header (magnolia logo) is generated to href='/' and the rest of the links are generated to '/*.html'. This happens when the generated link points to a site definition root node.
Changed link render manager from MultiSiteLinkTransformerManager to LinkTransformerManager and works in the same way.