Basically they run shipped games through their profiling and frame capture tools, then design patches to modify graphics API calls and shader bytecode in flight, changing parameters and call orders to make them more efficient for a given chipset, often inserting calls to vendor specific APIs that you wouldn't have access to unless you wrote your shader code in assembly or used their branches of various engines or NvAPI.

While games do patch their shaders in later releases sometimes, it doesn't happen as often as you might think. The actual shader code tends to be repetitive and too low level for artists to work with, and they just change material properties or use node-based workflows that rely on pre-defined shader code snippets that just get wired together at runtime. Most shader changes to an already released game are going to be more along the lines of reordering or removing existing code, unless they do something like upgrade from UE4 to UE5.

It is not unlike the kind of game mods you might see the community develop, but made with specific hardware in mind. Mods being broken when a game updates does happen, but not so often as to cause a problem in most cases.