Would be great if there is support between navigation of 3D content and VR headset.

If no support between them, there will be a virtual window embedding e.g https://threejs.org/examples/#webgl_decals , which is weird

ideally it would render stereoscopically but I imagine since most 3D applications control the camera themselves this will be difficult to make work across all things. 3D using css may work since it is up to the browser how it gets rendered.