This is a really interesting question, one I've thought about only a little. It has been useful to me, to first separate out the models, one being of meditation leading to the dissolution of duality and the other being of it leading to increased health. Then once there's a little room between them, so that meditation doesn't have to suffer under the burden of being everything to everyone, it is a super-interesting question. My personal sense, from what I've heard from Goenka is that he somehow confuses the models a bit, though what he is pointing to seems true enough. Certainly enough medical research has been done to show a positive physiological (and psychological) benefit from most kinds of sitting meditation. I've felt that in my own practice, just generally reduced levels of stress which I'm sure has some impact on health.
Also, the stuff Hokai mentioned about subtle energy practices seems an extremely ripe direction. Having done a little bit of taoist qi-gong, and also reading Ken Cohen's book, "The Way of Qi-Gong" it's becoming obvious that there are some very strong health benefits to doing these kind of practices, and that's actually what they're predominately used for. And then there's the integral approach that Hokai mentioned, of recognizing different bodies that one lives through and working with each of those bodies with the appropriate practices/methodologies. That also makes a lot of sense. If someone is suffering some physical ailment, I wouldn't send them to meditate first off, but maybe as a secondary option. That some people are cured of physical issues when meditating doesn't say much to me, except that it has some indirect benefits.
And then there's the dark night and all the havok it can wreak on one's life. I'm not sure if it messes with one's health, but does cause a lot of stress. I guess all of these points contain truth.