When I add a GameEngine object to a scene and view the SceneSettings.cs component on it I notice there is a Nav Mesh property that expects a Navigation Mesh. However those appear to be deprecated in favor of new component-based NavMesh Surface. For instance you no longer have access to the Navigation Static property too. I'm using Unity 6000.1.7f1 LTS and the AI Navigation package.
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The GameEngine object is used by 2D and 3D games alike. In 2D games, the NavMesh is defined with a Polygon Collider attached to a Navigation Mesh component, which gets assigned in the Scene Setting via the Scene Manager.
Indeed, for 3D scenes you do not have to set Navigation Static any more. A tutorial on using AC with the NavMesh Surface component can be found here.