Just marketing. I love starting up "The Movies" and getting Intel and ATI ads when I'm using AMD and nVidia hardware. It doesn't make a (noticeable) difference what you use, just as long as it isn't obsolete. There may be slight optimizations in some games, but as hardware from competitors improves and game patches are released, the differences continue to diminish, and in some cases, actual "best on" performance can become better on competing hadware.
Most of the time these "best on" campaigns come from game developers getting free hardware in exchange for advertising during the games start-up; reason being that the advertised hardware is the very hardware the game was built on. It's easy to say it "runs best on" this hardware when it hasn't been run on anything else. (Not that the testing department would let that happen.)
When you think of it, it's a great place to put an ad if you want gamers to see them often. The only downside is some games won't let us click past it. So I start to get angry at Intel, for example, because they're delaying my enjoyment of the game. Then it becomes a copycat of non-skippable DVD intros. And I hate those too.