Exactly. I do not see a down side to increasing the importance of winning a conference title.
The system described would have at least (16 x 12) = 192 teams eligible to be the National champion
My system would too, with a minimum of games. The best Non-Power 5 team automatically qualifies, although I would stipulate they would have to be ranked in the top 16, or else it would be the two best Power 5 at-large teams playing each other in the Play-In.