I'm not sure...Both those muscle groups work together to move the waist, dont' they? the sides and the back. I was never taught a lean in any techniques. When you say the same angle as the rear leg, you must mean in natural stance, I would guess. I have always practiced with back straight, both in karate and in bo jutsu.
In naihanchi, there is definately no leaning. The power comes from the rotation of the hips along with the rooted stance. Naihanchi is generally viewed as the foundation for shorin ryu, its stance-work and power generation.
With that in mind, I'm not sure what Nagamine sensei might have been talking about in that quote. The article doesn't really go any further into detail about it, about which one should be emphasized, if any.