The instantiation of NavigationModel in SiteNavigationModel is hard coded. So is the instantiation of SiteNavigationModel in STKPageModel So if you want to extend the behaviour of the navigation you have to extend STKPageModel, SiteNavigationModel, NavigationModel and in some cases NavigationItem, if e.g. you only want to override NavigationItem::isVisible().
The model class can be changed by configuration for almost anything, why not for the navigation?