I’ve never heard of Novikov before, but he probably doesn’t work in my area so I doubt I’d read his work!
Being 16 is probably the biggest hurdle for him… there are a lot of rules and laws around working with minors, and his presence on any university campus (esp. as a graduate student) creates a lot of work for other people. In many cases we are employees - paid by the university either for our PhD or for side work like marking and supervising (tutoring). That’s going to be more complicated for a minor. I’m in theory so I work with computers and blackboards, but I still had to do health and safety stuff and I imagine that’ll also cause more hurdles for a minor.
And, of course, a 16yo is simply a massive risk for any supervisor to take on. They’re far less experienced just by definition, have likely never lived away from home before, have never managed an adult life on their own before, and they’re still in the throngs of puberty hormones. A PhD requires you to be incredibly independent and unlike a child - I frequently have to sign off on things that your son would be legally unable to sign off on. It is completely different to undergrad and even most people 20+ will struggle, and it has very little to do with academic preparation. Could be very dangerous to begin at such a young age because it’s not designed for children/adolescents and academics will not be kind to your son. The rates of severe mental illness are high, ~70% qualifying for clinical depression or anxiety. People actually die. I wouldn’t blame a supervisor or program for rejecting a 16yo simply because they don’t want to subject him to that. When they damage many young adults, no one really cares, but it would be different for a kid.
The more “trouble” a student is going to be to accept and/or train (e.g. they’re a minor, they have a GPA below the cutoff, they don’t have the right background), the more amazing they have to be to be accepted. That is likely why your son’s supervisor told him to add more safeties - his age is a definite red flag and a disadvantage in applications.