Wouldn't that happen if you're running the proprietary drivers? I thought in general the proprietary drivers are built from the same core codebase across multiple platforms -- once you've gotten past the WGL, GLX, etc. bindings, and you have some system call for getting data to and from the card, the rest of the driver should be basically the same across platforms.
And similarly the games themselves are the same across platforms, apart from their end of the WGL or GLX or whatever bindings. So anything in the driver that says `if (!strcmp(name, "Portal 2"))` is going to be equally applicable regardless of whether it's a Portal 2 compiled for Windows, Mac, or Linux.
It's certainly a weakness of the all-free-software subset of the Linux platform (at least on Nvidia or AMD), but that's not the only option.