If there's a "negotiated" part comes from where the player is committed to play baseball. A guy can't be committed to Triton JC and ask for Harvard tuition money (though some teams have tried). They'll "negotiate" something like we'll pay the equivalent of Northern IL.
That's from 2016. The rules have changed and the negotiated language has been removed.
https://www.mlb.com/official-information/scholarship/reimbursement-guide-2017
The scholarship fund is not a negotiated part of the first contract. It's a separate piece from the signing bonus and every player regardless of round is eligible. Yes, Jerry Reinsdorf is paying for college for every player they draft along with every other MLB owner.
Every draft pick is eligible for the MLB schlorship program which pays 100% of college tuition. Players in High school, junior college, and college. Some teams will even pay for grad school. Baseball is not forcing anyone to give up their education.
He's not going to miss much development time but there are other things here to woory about. I don't like the small frame, the max effort level and that he was also hurt his sophmore year. He has a pretty big hill to climb.