You do know pro players have been signing endorsement deals for over half a century and not run into ANY of those problems right? So back in reality, none of those are problems. What is a problem is propping up a multimillion dollar league on players legally banned from making money.
The NFL functions as a monopoly, with teams limited on how much they can spend on players, and control of where the players go. Each year, they draft the top 400+ players.
Most revenue is split between the teams. That's why lousy teams like the Browns and Lions don't go out of business. They're guaranteed a profit, no matter what they put on the field, and with the rare exception of a star who is released or runs out his contract, other entities can't sweeten the pot, cause players are bound exclusively to one team.
In colleges, it's a whole different animal. Think Nike offering an endorsement deal if you sign with Oregon, or UnderArmour doing it with Maryland. Think one college having a $10 million a year booster offering endorsement contracts, with no limits on amounts. Most colleges will get priced out of being competitive.
FWIW, approximately 8% of athletic departments make money. For the rest of them, they're losing money trying to keep up with the "big boys."
What you're suggesting won't go like the NFL, it will be something different. I don't know exactly what it will look like, but whatever it is won't be what we're expecting.