It could also work in case you needed a non-linear level design where many gems lead to one waypoint - a hub of sorts:
And, finally, nothing stops you from having many waypoints and many gems in a single actor - interlinked any way you need. Perhaps the teleport locations are random (pokes @Zof)
Think of the waypoint gem actor as a manager blueprint that controls where the player goes. How to go about it depends on the scope, ofc.
Good luck!
On the other hand:
unless I set the waypoint actor on the instance
This is one of the better methods actually.