I suspect that the checkpoints rendered in the editor are actually a bit bigger than the editor wants me to believe. I noticed it when editing tracks that produce at some point the “wrong track” message. When I examine the track in the editor, the rendered checkpoints close to the point where the message appeared do often not touch the other road part. One example is the first version of Winding.
If I am right, we would also have the explanation why the mistake with checkpoints collisions is common.