You also need to do a cost benefit analysis. How much merit do you need to apply below his stats. Will you turn down a top 10 college in his area of interest for 20k off tuition at a college ranked #50? (using that as an example since I do not want to name specific colleges but not talking about getting a free ride to Vandy).
I know personally NMF and Intel finals (girls in STEM so an advantage there) who did not get the scholarships at Duke, Vandy or WUSTL. If your son gets it great, he will be a candidate who can probably get into a HYPS. Obviously no one knows at this point. By all means apply but that is not where you should be focusing.
What you should be doing is getting him used to the idea of merit. That his goal is not Harvard but a free ride at a place he is comfortable. I made this mistake with my kids.