@Mopetenpit, That is an intriguing question... 
I am quite confident that the stored coordinate is the one that represents the WP and not the black dot. That is easily argumented, because the WP comes back at the same place when exporting and re-importing a GPX file. The black dot is a calculated coordinate that fixes the WP coordinate to a routable road.
However: because I hate to talk bullshit I actually exported a GPX file to check if not also the black dot coordinate is present in the file.
Each WP seems to be represented by a single coordinate in the route data of the GPX file, but I had some trouble recognizing it. It seems the coordinate in the file has a lot more digits than the ones shown in the WP info in the planner
(red oval)


If you look at the Track information in the same file you can see that the first coordinate (green circle) is not equal (besides that LATitude and LONgitude have been flipped? Why...). This is quite logical, since the breadcrum over the routeline is represented, and not the waypoints. I think for at least the first and the last WP of a route the track-coordinate will be exactly the black dot. How the breadcrums in between these point are calculated, I have no idea. But for the start en endpoint I checked them in Google maps and they seem to correspond. Just flip LAT and LON, else you will and up somewhere off the coast of Somalia... 