I'm more inclined to believe that what you see in the game is better indication of canon than the mission file.
Yeah, it was PLANNED for it to have a waypoint path and stuff, but the thing is, you look at it in game, it says it's disabled.
Therefore, canonically, it is disabled.
Regardless of what reasons, that is all a normal player would see. A non-modder would
never see the waypoint paths intended for it.
I
know that it had other things planned for it, but it's disabled in game.
Besides, we were never told by
that the waypoint paths and stuff were what the mission was intended to be. Perhaps the changes were intentional?