Earlier quoted context omitted.
They're precompiled for the console GPU architecture, not the PC architecture, so they can't be used directly and still need to be emulated - I think those precompiled shaders are the input to the ubershader.
The GAMES THEMSELVES are precompiled for the PowerPC architecture, not the PC architecture, though. That didn’t stop anyone from creating Dolphin. GPUs (I’m told) have far fewer instructions to emulate than a CPU, so I’d think that low level emulation of the Flipper shaders would be no trouble. Can’t translate or transpile them to PC GPUs though because those instruction sets are somewhat secret, I think. I know noth…
The GPU ISAs are known (e.g. the PTX compiler for NVidia is open source and has a backend in LLVM). The main problem is that the GPU ISA changes with every GPU hardware generation and manufacturer, so if you want to support Nvidia 3xxx + 4xxx + AMD VLIW + AMD GCN + ... you have to use the common demoninator GLSL/HLSL/SPIR-V/whatever.
> why they didn’t emulate Flipper at a low enough level to use the precompiled shaders directly.
They did. Originally the GPU emulator was done in the CPU, and in 2017, the GPU emulator itself was moved into a shader ("ubershader").
The console game itself does not include shaders in text format like many PC games do.