You have an academically advanced, projected smallish player. He may, or may not, find that catching is his best ultimate position - assuming he remains committed to baseball. He is able to play with older kids (thereby demonstrating that his social interactions are perfectly age normal).
You have no control over his final size, nor the age he will reach that. You have no control whether coaches will have a bias against players his size (and that would not be all coaches; I saw a D3 game this past season where the starting catcher was 5' 3". The HC of Nevada was a fabulous 5' 5" second baseman in his day.).
What do you control? You control the age he is for future grades; hence the original question. You control the amount of effort he will put into school and future standardized test - gatekeepers to some schools.
While the decision to "red-shirt" a kid before HS isn't cut and dry, in your case (IMHO) the balance tips to NOT holding him back (academically advanced, socially able to interact with older players, but small body with limited physical projectability).
If he has superior baseball skills, superior grades, superior test scores, the high academic type schools (Ivy, Patriot) would be a possible target. The higher you go into the academic pyramid, the fewer the number of players who meet both the academic and baseball skill set requirements. (I'm assuming that he will play in HS and run the gauntlet of showcases, lessons, etc..)
So, I would stop fretting about what you can't conrol (my S was 5'4" 125 lbs as a freshman, graduated at 5' 11" and 145) and hammer what you can control: working on the baseball skills and academics with equal fervor.