The Application object is in no way hidden, though its role has been reduced to the point where it is no longer required to create your own sublcass of Application.
There is still nothing preventing you from creating your own subclass of Application and providing a reference to it in your portlet configuration in exactly the same way as with Vaadin 6 though you shouldn’t create the UI in the init method now that you also have a subclass of Root defined in your configuration.