I still say this is trouble. There's a very good chance that this will mean that the Big 12 champ's best win will go from being against, for example, a top 10 team to, to being against a top 15-20 team. In other conferences that's always a possibility with the championship game. With the Big 12 it will almost be a certainty that there will be a significant drop for one of the teams since between the two best teams, there will have to be at least 2 losses, not just 1.
Like I said, the SEC already has an advantage in that they have 14 members, which means the lower half can divide up the losses among themselves more AND they get to dole out more losses to OOC teams with 4 OOC games and most teams playing 3 really easy ones. The strength of schedule in the Big 12 is at a complete disadvantage already because you only have 10 conference teams to divvy up the losses to, and 9 conference games. It's probably a clearer way to determine the best team in the conference, but the statistics aren't going to look as good. It doesn't help, either, when so many Big 12 teams have the stubborn habit of scheduling some of the same OOC opponents in the same season (though, luckily we didn't do nearly as bad with that this year, with only SMU being on the Big 12 OOC slate twice. Even still, that means that, best case scenario, one of our OOC opponents has 2 losses from us before they even start their conference play, when an ideal situation would be for the to get 1 from us and then win as many other games as they can). Strength of schedule, based purely on opponents' wins and losses is a fairly standard thing to use (even though there are plenty of arguments about why it doesn't make sense when you consider the different levels of competition for said opponents, and, like I said, things like round-robin schedules and smaller conferences). It doesn't work in the Big 12's favor at all right now.
It will be made even worse if one of the best teams that the champ played suddenly isn't just a 1 loss team, but a 2 loss team. Or not a 2 loss team, but a 3 loss team. And so on. And opponents' rankings suffer as a result as well. "Their best win was against the #6 team in the country!" sounds a lot better than "their best win was against the #14 team in the country!"