Yes... conference champions definitely get a slight boost now... but the past few years the favorite has been winning the conference championship game, which gives the perception that the teams selected will only be conference champions. However, if the underdogs wins more frequently (like they have many times before), then 2 teams from the same conference is actually very likely.

Take this scenario. Alabama goes undefeated and Auburn has 1 loss. Let's say a 2 loss Wisconsin beats a 1 loss OSU in the Big 10 championship game. Let's say either the Pac10 or the ACC or the Big12 doesn't have any teams with less than 2 losses. There you have it... 2 SEC teams in the finals. You can change the conferences as it doesn't have to be the SEC... it could be FSU and Clemson.

That's not a stretch, so let's not get too caught up that it is "doubtful". I think over the course of 50 years, you'd see 2 teams from the same conferece 35% of the time... or roughly 1 in every 3 years.