According to Macrumors, there is a compatibility issue which means Nvidia might be out of the picture for a while. Nvidia is only capable of driving dual 5K displays with the Polaris GPUs with DisplayPort 1.3 which is not supported with Thunderbolt 3.
That makes a lot of sense, but I haven't seen any hints that it's coming soon. Keep in mind, you really need an upgradable GPU for that, since these $1000 5K displays have a long life cycle.
And it would probably require rewrites of high-performance apps and games to be something closer to client/server setups to manage communication between the CPU/memory and GPU.
There is really no difference for anything but the most demanding applications though.
5K displays won't cost $1000 for much longer. Right now they are premium products but soon they'll be the norm. By then, adding a good enough GPU to the screen will make sense (because your laptop doesn't need to carry - and feed - more brains than needed to push pixels to the built-in display) and, if the user wants more, they'll use whatever is installed in their computers.
http://www.macrumors.com/2016/11/14/late-2016-mbp-amd-gpus-s...