I think you hit the nail on the head. Let the NFL manage it. CFB has no experience with managing free agency, unions, etc. create an NFL - College Div and let them deal with it. It has become a cesspool.
I mean there probably is room for an NFL farm league of 12 teams. All restricted to players age 18-21 (not sure of 32 is doable without a lot of dilution) these teams play in NFL cities (Jacksonville, indianapolis, phoenix, Seattle, Nashville, NY/NJ, Charlotte, Cincinnati, San Francisco, Tampa, Pittsburgh, and Kansas City)
Call it the NDFL (National Developmental Football League). Each year the NFL teams hold a draft for the best highschool talent just like the MLB draft. Kids have to declare for it BUT it does not preclude them from getting scholarships to college until they sign the contract. The players are then placed on farm teams by the organization that drafted them. This can change yearly based on the teams wants or needs.
Each season is 11 Games each team plays each team once. At the end of the season the top 4 records will play a 2 game playoff.
Each team has a 60 man roster and 10 man practice squad, teams can backfill from other practice squads.
When a player is drafted they sign a developmental deal. This deal locks them into the NFL team drafting them which basically guarantees a payout at the end of the contract. If the player plays all 3 years they are owed either a buy out (negotiated) or a fully guaranteed 2 year contract.
Teams have a developmental contract cap.
All developmental players are paid the same rate negotiated by the NFLPA While they are on a developmental roster.
Modified rules exist
Kickoffs are limited to after TDs. (Field goals result in the opponent starting on the 25) Justification is to limit hits without removing the looks completely for returners.
Full punting and Field Goals, XPs are kicked from the 10 yard line instead of the 15.
Two feet down on possession.
Targeting is a 15 yard penalty, 2 targeting fouls trigger a fine. and then on each subsequent fine.
Celebrations are allowed.
Players have Snap count limits (50 snaps a game) this is more to protect the players than anything else. This also gets more opportunities for eyes on players. Snap count limits waved in the playoffs.
Note:
Totally didn't put a team in atlanta for reasons.