Nothing really changes. The NCAA is not some autonomous entity that sprung up and took over to run college sports. It is literally the member Universities own committe formed years ago to do that. The conferences are the same thing just on a different structure and they'll still have to manage all the different issues (tournaments and schedules, TV Contracts, players eligibility, other rules and regulations for compeition, maintaining competitive balance, etc) just like the NCAA had to try to do.
It doesnt matter what you call whose running it, the question is will it in the end have anything left to do with student athletes or COLLEGE athletics? Probably not.