That reg is referring to the door window area only, not the quarter glass. Its intent is allow ducting while limiting one's one's ability to one, block off the window for aero improvements and two, minimize obstructions for safety workers getting to you through the window in case of incident (thus the "It is not permitted to otherwise fill in the window area" notation.)
Further, a quarter glass is not a "driver and/or passenger window area". By definition, a quarter glass cannot ever be a "driver window area".
Thus, this reg does not allow a quarter glass to be replaced/modified. If it did, then a lot of people would be dropping some weight off of head height be replacing the quarter glass(es) with Lexan and putting in a crappy ineffective "ducts". I certainly would.
GA