Waypoints become available in a level once at least one waypoint has been unlocked. However, there are no waypoints in the end game level, so the waypoint button does not become available.
You can override this by adding a waypoint, but that would only allow you to teleport inside the end game level to this way point. In the main campaign, all waypoints in other levels get locked as soon as you leave a level. Several other things also get finalised when leaving a level, so teleporting back and forth between levels is likely to result in various unforeseen consequences.