SluggerDad,
When someone uses the terms high skill but physically underdeveloped, I think of someone like Richie Pedroza. I don't know his weight when he started at Fullerton, but as a senior he was listed as 5'6" and about 150lbs, and he might not have been either.
He also was probably the best baseball player at Fullerton during his last 2 seasons.
I use Pedroza to suggest that as with all of us parents, their might be some rose colored glasses in how you are reading your son's evaluations.
With that background, I don't think your answers are D3 vs JC. The questions I think your son needs to answer including the following:
1.) How important is his education?
2.) How important is baseball?
3.) how does baseball rank with education? What opportunities do his current grades and SAT/ACT scores open educationally? What doors could baseball open to possibly enhance the educational opportunities?.
4.) Which coaches who have seen him "believe in what he can do" as contrasted with emphasizing what he cannot do? Nearly every player in HS who is not at the elite level is told to get bigger, stronger and more explosive.
5.) Of those coaches, what is their history in developing players during the time the player is with the program? There are JC and D3 coaches who excel in developing players and their talents and skills as there are at every level of college baseball. There are JC and D3 coaches who don't, just like every level of college baseball.
6.) How capable is your son of working through adversity, slumps, injury and intense competition in the context of being away from home in a college environment and all that involves(classes, grades, parties, social life, early morning lifting, long practices, distractions of every type and new freedoms which challenge most every student.)
Of course I have never seen your son play. From everything you have posted in this site which I have read, my objective sense is that his physical size is not the only factor impacting his talent evaluations and college recruiting. He has had a ton of exposure just since you joined this site. When looked at objectively, that amount of exposure as contrasted with interest of the college coaches is probably the most accurate assessment of the level of talent, no matter what is on the paperwork.
Finally for your perspective, the next 4 years of college baseball and development are largely going to be determined by your son and how hard he is willing to work and sacrifice in a college environment. You have to be willing to let go of what you want or what you see. What will happen is what your son works to make happen on the field and in the classroom, with the one provision of making a solid choice at this point on what coaches believe in him and what those coaches have done with players in their program as the track record.
I hope some of these thoughts are helpful. Certainly, there may be some some "tough love" tone but your son does not have a long time to make some very important decisions and judgments, based on being really candid with himself and his parents.