The question of whether or not fans will lose interest if their teams are not a part of one of two power conferences will depend entirely on the structure of the playoffs. If, like the NCAA basketball playoff, cinderella teams have a shot at winning it all, fans of all teams will stay engaged.
This is where the CFB playoff needs to go to 8-16 teams to allow for 2-3 non-P5 teams to be included. That way non-P5 games don't become basically irrelevant and fans stay engaged. Make it so that any FBS team with really good players and good coaching has a path to a NC and fans will stay engaged, allowing the CFB and the NFL to co-exist.
Obviously, the money gap hurts the chances of a cinderella-type football team winning it all, but time will tell if that gap ends up hurting the sport on the whole. Will NIL have a leveling effect? Or drive players to the teams with the largest markets/fanbases? I think in a few more years we will know the answer to that.