Still having problems with this, but I've narrowed down the behavior a bit.
So when you do LockWaypoint(""): The waypoint is still present on the rift travel list.
However, if you save your game and load it - the waypoint entry disappears. This is the only way I've found to make it work. Even a level transition will not do it.
This doesn't really help since you could theoretically play for hours without loading and still use the waypoints that are supposed to be locked.
