You're talking about using vendor specific extensions in DX/OGL, of course one card is going to be favoured if you use them, and there's lots of games that had an ATi bias where nVidia cards still out perform ATi. Vendor specific extensions are retarded and shouldn't be used, it defeats the purpose of using API abstraction. If you want a more advanced API, then use an advanced API (like DX10 or OpenGL 2.0). If you absolutely *need* vendor specific extensions then optimise for both.
That's faulty logic, it's like blaming x86 for not running PPC code properly, and I certainly wont make my purchasing decissions based solely on one software product that's not even released yet. Maybe if it was some super-efficient, compatible, and stable Operating System that requires a particular CPU, then I'd do that.