It simply doesnt matter if a player is at a D3 or a D1: if he has pro-potential he will be found and drafted/signed. It doesn't matter whether he plays in a college quasi-MILB stadium or on a field without dirt basepaths, he will be found.
(If the player won't start for a "low HA D1" he's not likely to move to the next level, anyway.)
If baseball has earned a player the leverage to get admitted to that HA school (regardless of division), the family has done its job. [And the HA definition I'm using is extremely narrow.]
Focus on the opportunities a college offers him for life after college: internships, grad school options, employment options. Focus of what the college offers him during college: being taught to critically think, being taught to communicate clearly in writing and orally, fulfilling (as best as possible) his intellectual potential, becoming a leader, finding and exploring new heretofore unexpected interests, socializing opportunities, building post-college networks, and the rest which matures him. That is what a decade of baseball focus has earned for the overwhelming majority of college players; going pro is for a small minority (and within this group the vast majority will be working in the real world within just a few years of the draft, anyway).
Where will your son thrive (as best can be guessed for a teenager)? Some in small LAs, some not; some in rural areas, some in cities.
Baseball got him there, so figure out where the best springboard to his intellectual success and future employment lies.
Imo.