A playoff (and for that matter the NCG) doesn't necessarily mean the 4 best teams, it means the 4 most deserving teams with all things considered. Ideally the 4 most deserving are going to be the 4 best, but it certainly doesn't have to be that.
If those 4 finish unbeaten they will clearly be the 4 most deserving and might actually be the 4 best. With just 2 teams, I think you could easily say 2 highly deserving teams will be left out, but I believe in most people's eyes the 2 best (Oregon and Alabama) will be playing in the game.
Oh and Alabama is the #1 team in the BCS computers, not just the human polls, so I'm not sure why anyone would think they wouldn't be #1 if not for the preseason. Also, by the end of the year Oregon might very well be #2 in the computers.