Apple's customers don't care about NVidia -- they don't do serious computation, scientific computing. Our Hollywood clients all use PC-architecture machines with NVidia for video editing and rendering. The writers, etc, use Macs.
So Apple can save the cost and get higher profit margins by not having powerful GPUs in their products.
I know a lot of VFX and animation people that do serious rendering / ray-tracing computation and do wish they could use nVidia GPUs in their Macs. It's worth considering how, unlike writers, rendering needs machines not just for all the animators, but for the render farms too.
So Apple can save the cost and get higher profit margins by not having powerful GPUs in their products.