I'm an XC coach, and I've worked with a good number of athletes.
On the LR boards, there is an almost reflexive belief in equal trainability for everyone. Personally, I think it's because this board is demographically skewed towards very talented runners, and talented runners like believing that their success is due to hard work more than genes.
The gods of running did not align talent with desire, nor did they align desire with trainability or durability. Your son may want it badly, but may have been born with genes like mine--solid, but not spectacular. YOUR job as a dad is to SUPPORT your son.
I've seen it work both ways--he may physically mature, lay on some miles, and drop 16:xx's his senior year. Or he may struggle to improve as he lays on the miles and stay in the 18:xx's. On our team right now I have two athletes who train side-by-side who embody this phenomenon. They ran together all summer, dramatically different results. They have done virtually identical training since 8th grade when they both had similar times. One runner is a mid-16'er. The other is an high 17'er. Some bodies are just different than others.
Be PROUD as a dad you have raised a 16-year old capable of such commitment, and SUPPORT whatever results come from that commitment. DO you know how few of today's kids can see tough training goals through like your son can? When he is an adult, this discipline will suit him well--very well. Unless, that is, he internalizes a narrative that nothing he ever does is good enough, which he WILL pick up if you give him that message.