I am dubious that yoga, even Yin Yoga, can develop the bones enough to close the gaps that cause Spina Bifida. As you say, yoga will increase bone density, but a drastic remodelling of the shape of the bone is a different proposition.
Bones can change shape over time, but it requires a lot of time and a lot of stress. Think of braces for teeth. It can take years to change the shape of the jaw, an even then, many people need to continue to wear retainers forever, because the jaw wants to revert back to its original shape. I doubt the boy would want to wear a spinal brace for years (even if this was feasible.)
Local remodelling of bone can occur at attachment sites of tendons. For example, the lesser trochanter on some people have a pronounced bump, due to constant stress of the iliopsoas (often found on marathoner who do a lot of thigh flexion.) The challenge with Spina Bifida is to localize the stress to the few vertebra that have too large of a gap between them, thus allowing the spinal chord outer layers to leak outward. Yin Yoga will not apply a direct stress on those disks as long as braces will. Nor would we be able to stress the muscular attachments/tendons enough to remodel the vertebra.
In short: I doubt that yoga can create the changes you are thinking of. It would be interesting to hear from others who have this condition, to hear of their experience. However, yoga can definitely help to deal with consequences of Spina Bifida. Check out this article on Yoga Journal, for some examples.
http://www.yogajournal.com/for_teachers/591
Often, in cases of SB, it is very helpful to strengthen the back muscles around the affected area to improve posture and take stress off the joints. Yang Yoga can definitely minimize the effects of SB, but as always, the student needs to work with his doctor or therapist to make sure that yoga won't make things worse.
Finally, puberty is a time of significant bone development and his condition may change considerably during the next few years. It may be best to wait for the bones to "settle down" and see what his situation is like in a few years, to then determine any future yoga program.
Sorry I couldn't be any more helpful.
Cheers
Bernie
Ps - While not dealing with SB directly, there is an inspiring yoga teacher, Matthew Sanford who has used yoga to help with spinal injuries, including his own. He has a book,
Waking: A Memoir of Trauma and Transcendence and a web site that you may find educational.
http://www.matthewsanford.com/