Non-authorative answer but JSF 2:s navigation has been enhanced to the extent that I would think it's easier to use a custom navigation handler for Seam 3. I'm not aware of the technical reasons for why things were implemented the way they were in Seam 2. With auto-registering filters and listeners in Servlet 3 (and CDI-style interceptors/decorators), I would think that the amount of stuff you have to place in web.xml yourself will be kept to a minimum
Mistakenly I suggested that Seam does't use the standard extension mechanism for navigation handlers. In fact there is SeamNavigationHandler and it is in the faces-config.xml shipped in the jboss-seam.jar which obviously provides the default configuration for Seam projects.