Shader replacement was extremely popular for years - see AMD's infamous Doom3 shader replacement: https://www.anandtech.com/show/1488/6 . NVidia drivers did the same thing although they were (generally) a bit smarter about it, relying on shader fingerprinting rather than application fingerprinting to prevent embarrassing "rename the EXE" expose articles. They were notoriously caught using a benchmark's camera path as a fingerprint: https://www.extremetech.com/computing/54154-driver-irregular... .

GPU drivers are still loaded with such replacements, either to work around bugs or to optimize games where a developer partnership was impossible or otherwise rejected. I think that with the shift to lower-level GPU APIs this practice is beginning to fade, but it's basically been par for the course since programmable shaders became a thing.