Your son's situation is similar to my son's when he made his decision a few years ago (although he is a position player not a pitcher). He chose a HA D3 and loves it.
A few thoughts based on your OP. It sounds like your son's priority is (1A) academics, and (1B) baseball. My response is influenced by this. I think something he should consider is the challenge of balancing the academic schedule with his baseball schedule. A D1 schedule averages ~56 games in the spring. A D3 schedule is 40 regular season games plus any playoff games. Travel to away games is usually more local as well for D3. There may be an early spring trip to Florida or the west coast for a week of games but that typically the extent of travel. As for the fall, they will have morning workouts 4-5 times a week at 6:30 AM. I don't think that is any different than D1. However they are more limited to coach led practices in the fall.
The quality of talent that we see at the HA D3s is outstanding (this was one of the most unexpected things for me). Most pitchers consistently throw 85-87 and you will see several guys throwing 92-93 with schools at the top conferences.
Good luck at HeadFirst, they do a great job. Your son should take advantage of interacting with the coaches. He will have access to them during games on the field and in the dugout unlike any other showcase my son attended. HF was where he received the most real interest from coaches and was also the showcase that first started his communication with his school.