Dave, I suggest that PF3 should not create XXX waypoints between the last user waypoint and the destination, even if they should have been there. Optionally warn the user about the last waypoint being too far away from the destination.
XXX entries NEVER appear after the last waypoint if IT is at or above the control centre handover altitude, which really your last waypoint shouldnt be.
I think we all agree that the flight plan is not good, but if you load it (it is included in the Logs.zip on page 1), PF3 does not complain and automatically generates this: