You've raised some valid points, but just because the NFL has it set that way doesn't make it right. Fans still complain when a 7-9 team is not deserving of being in the playoffs. In fact I heard some broadcaster's complaining about it on the radio this weekend.
I still don't believe an 8-5 Northwestern team would deserve to get in the playoffs over 12-0 UCF, a 9-2 Army, 10-2 Boise St, or a 10-2 Utah St. If that were to happen, you can believe that Michigan and Ohio State Fans would be complaining insistently, as they always do. If you have to put the caveat of top 12, I believe that it would do as I said previously, and erode the importance of the conference championship.
Although this is not perfect, I think the current way is the best way to ensure that the sample size is small enough to make it matter ensuring quality games, and not take away from the bowl games.