I'm not knowledgeable enough to know the answer. One thing that is different with Dolphin is, that the hardware they emulate is known and the games itself do not change with updates either. So they semi half-pre-compile them maybe, so the rest of the compilation process for your hardware is less work? The Gamecube games itself doesn't have any Shaders to compile, so there is nothing in the system implemented to compile. Dolphin itself introduced this step.
Meanwhile on PC, the entire GPU and driver architecture provides steps to compile. The developers just don't do it properly, while SCSKiller does the job the developers would have done; by asking the GPU to compile what the game should do.
I don't fully understand Ubershaders, even with reading parts of the post. So I don't know if this could be applied to generic PC games where the hardware is completely unknown and the games get updates.