Steve, this is an excellent topic to bring up. Getting a proper looking window for 3D purposes and for CD detailing has always been next to impossible. Even though VW ships with the Marvin window line, for example, no Marvin window has a sill configured like what we have to work with. Cutting a section through a window is of no use in a developed wall section and I alway choose to turn off the window object in such a section in order to insert manufacturer's details I've downloaded. I agree with your points about how a sill should align relative to the frame.
Things get even more weird when one opts for showing trim under stool and/or sill (the trim clips up through the sill at either side), or when the splayed wall feature is used and you can't control the length of the sill on the splayed side independently of the length on the other side, so one side has overly long sill extensions.
If one chooses to show interior and/or exterior trim one would expect to see the edges of the trim offset a fraction of an inch from the face of window frame but this can't be controlled and so again a useful plan detail can't be derived from a jamb location in the model.
Options for brick and masonry sills also are problematic but I don't wish to go on and on. Wes, hopefully your "in" with the window guy at Nemetschek will lead to something helpful. ;-)