You are correct, and you make some good points.
But left out of all of these lawsuits and discussions is player input.
Suppose the players unionize, and start collective bargaining?
One of their bargaining positions could be limiting distance traveled for conference games.
They could very well have a say in how conferences are aligned in the future.
I think you are right about the players getting paid and it probably will have to be collectively bargained. But, I think this will only apply to top division of college football. I think the upper division (currently called the SEC and Big Ten) will have professional players with contracts and rest of the schools won't pay their players.
There will be a clear demarcation between the upper division and everyone else and they will probably be governed separately, have separate playoffs, etc.
I don't even know where conferences are going to fit in the future.
For that matter the SEC and Big Ten as we know it could also be "doomed" in that they might not be called that anymore. The SEC and Big Ten (and whoever else they want) could be governed by same body.
Looking farther down the road, I wonder if players in the future will even have to enroll in the school they play for. They could just be hired to play for Alabama Football Club, for example. Why just 4 years? What is eligibility? Who knows...