The Waverider Waypoints themselves only have one known purpose. They can be activated to summon the Waverider to the player's location. The structure itself resembles a Four-Pointed Star surrounded by a wheel. Much like Teleport Waypoints, the Waverider Waypoints glow red when unactivated and blue when activated.
Since they can't be used to teleport yourself to it, and you need to be close to them to use them, whether they are activated or not makes no functional difference whatsoever, other than the Primogem awarded on their activation.
Waverider Waypoints can't be activated when they are too far from water.
World Map Description
A device with mysterious power that is typically located near the water.
Can be used to summon a Waverider to your side. It can be regarded, from a certain point of view, as a "Teleport Waypoint for Waveriders only..."
This device has a mysterious power.