The programmer of a modern PC game knows that they will be using shaders, and can arrange for them all to be compiled and sent to the GPU during a loading screen. That eliminates the lag, because there is no delay when choosing which shader to use for the next triangle. On the other hand it makes the loading screen take longer.
Meanwhile the programmer of a console game, not using shaders, could set GPU registers to any configuration they wanted just before rendering the next triangle. You have to actually play the game to find out what configurations it programs into the GPU, because those configurations are not neatly organized into a set of discrete shaders. Even then there is no guarantee that you found all possible configurations used by the game. The videos in the article provide a good example: the player fires a gun with luminous bullets, so on that frame the walls and floors need to be rendered with an extra light source. That requires reconfiguring the GPU to take that light source into account, then changing the configuration to render the weapon itself, then changing it again to render the HUD, and so on.
Now imagine that you go to a place on a different level where the walls are not shiny, and it doesn't bother to render the walls with the extra light source. Or it renders them with extra vertex lighting but not extra specular lighting. Now combine that with every type of wall and floor in the game; they might all need a unique shader to be lit correctly by that one gun. To find all possible GPU configurations you need to fire that gun, and every other, near every single different type of wall and floor texture used in the game. And there are a dozen different guns.
And then you need to do it all again while wearing the night–vision goggles, because that causes everything to be rendered with a different configuration yet again.
Every one of those unique combinations needs to be made into a shader, and there’s just no way to be sure that you have actually collected all of them. Or you can write a single Ubershader that can, by using branches, loops, and other advanced tricks, emulate the entire capabilities of the emulated GPU. Then you can program the Ubershader by sending all of the emulated GPUs register values as uniforms.