The gi pants rub on the floor and the knee skin gets a good stretching.
The hakama rubs on the floor, the pants slide a bit on top of the inside of the hakama, and the skin doesn't get as much stretching.
That's my theory, and I'm sticking with it.
It's similar to wearing two pairs of socks when you're hiking. The hakama definitely reduced the discomfort of doing suwariwaza. Another benefit I find is that I don't have to worry any more about my belt coming untied!