If the distance at which it registers as "visited" could be modified, then it might work. Thankyou.
That value is hardcoded, 1000 meters it is, though this is pretty close inside the FS-Universe. I think it would be useable for your cause.
If you need any help setting the waypoints up, I can give you a hand (and can also provide a tutorial if you want).

However, the 1000 meters are just the value for "nav visited", that means when the navpoints get's marked green. You can still make SEXP's
and check the distance (i.e. if player is closer to 500 meters, then let ship warp in).