When you set a waypoint as your navigation target in the map view it would be nice if there was some way for kOS to get this waypoint similar to how you can get the target.
A skim I did through the KSP API documentation and the mod waypoint manager and it looks like there is a class NavWaypoint class that may contain the needed info also might be something attached to the vessel for getting the waypoint called navigationWaypoint as well.
I would personally expect the use this to set or get the given way point would be similar to the use of the target bound variable using some var name like waypointtarget