More than likely the internal rotation comes from his thigh bones (femurs) being internally rotated in his hip (acetablum). It's known as hip dysplasia.
Me and my sisters have it and I've noticed it in my two boys, too. At some point, orthotics for his shoes would be helpful. Ballet helped me considerably, but that doesn't always seem like a viable option for boys.
Chiropractic can help some. Some chiros have thier own orthotics they sell. Foot Levelers is the company most of them use. I use the Foot Levelers as an adult and I really like thier shoes and inserts (but I don't wear them much all summer long as I still love my flip flops).
Anyway, it's genetic. You can't fix it, just help it. The worst of it is the back pain and the difficulty when pregnant. At least our boys won't go through that!