GPU vendors don't have to hook rendering functions since they're the ones providing the implementation of those rendering functions.
If Nvidia requires extra hooks into the game they usually ask the developer to call certain functions in NVAPI, which is their vendor-specific driver interface.
There must be some kind of whitelist system. Discord for example doesn't have many options to draw it's ingame overlay. They either create a topmost transparent window (does not work in exclusive fullscreen) or hook glEnd() of the targer or however it's called these days.
