I think it's do with how the way games are coded on console. Because there are lots of specific optimisations, if the console suddenly starts executing things faster, it can break timings or something. It must have been trawling through pages of gaming news that I've read this. Whether it's 100% accurate is another matter.
It all depends how the game is programmed. Consoles will usually target a fixed framerate, because the hardware is constant and the framerate is constant, you just concentrate on wringing every last bit of performance out of the milliseconds you have available.
As the PS4 Pro has a proportionally faster GPU than CPU, games that were targetted at just the PS4 won't just automatically scale up on the PS4 Pro.
Going forward you'll see more developers targetting the base and Pro systems more effectively.