If I was in your shoes......
Your son has a "hook" with his academics. If he really wants to play college baseball he should be calling some of these high academic schools to see if they will allow a late application. If they allow it, I would also reach out to the coach to take his temperature. No guarantees. My assumption is the smaller the school, the more flexible they will be. Yes, it is a tremendous longshot.
The bottom line is your son will be trying to walk-on somewhere if he really wants to play college baseball. My point is if he reaches out to some of these other schools, it could possibly give him more choices. Again, he has outstanding academics so use that as leverage.
The ND scholarship sounds like an outstanding opportunity. Good luck!
BB, here's a link to a recent post by one of our members who put together his own "D3 Academic-Baseball College Ranking". With your son's grades and ACT score, I would think some of these smaller high-academic schools would have flexibility regarding a late application. Seems like a perfect fit for your son if he would consider those types of schools. Good luck.