nUI doesn't change the bars. The bars you see are 'copies' ( I hope I worded that right Scott ) of the blizzard bars. Blizzard only changes the bars due to spec changes and the main action bar on stance changes ( apart from a couple of stances on certain classes ).
Addons like Bartender actually coded their own action bar functionality and took more direct control over how they work and I think Scott was trying to avoid that so that things were less likely to break come patch time ... erm .. kinda like what happened with the chat frame due to blizz changing names on us
