Ah, that's when it becomes complex. It depends on whether or not the app display is rendered on or off screen. In the case of the iOS UI, it's rendered on screen, then down scaled for the 6s Plus. And these results are all from the same version of the GFXBench app.
It's fine if you don't notice any stutter or difference, but many people do. Turn on reduce transparency, and launch a 3D Touch menu. It's definitely smoother than with reduce transparency off. There is absolutely a difference between the 6s and 6s Plus if the content is being rendered on screen.