and of course teleport pads (not sure about waypoints so muhc) can be made vertically. You can even make them in the ceiling since they are the activation only. The waypoints are the only things that need to be below where you want to spawn.
I have conceieved of but not build rooms where the four sides and floor are all teleport pads linking to other identical rooms, providing a teleportation network around the world. Would they be public? probably not.. removing one block from a rune can fuck it permanent and require re-signature aquisition...