I've also seen problem with host-node map. There needs to be a function that returns a url to a node that takes into account host-node map and it needs to be used in places that create absolute urls. There are other problems also like you can't get to api-doc anymore. To make it really work would be a lot of work. I use the main site only for adminstration and use host node map subsites that don't require a login. It seems to work fine for that.