I think you should be able to set tardis waypoints using a 3x3 multiblock structure like the galacticraft rocket platform seen here

to set the waypoint you should have to right click it with a tardis is key, this would bring up a gui where you  can name the waypoint and set the privacy

In my oppinion this would be better than be able to set waypoints everywhere because you wouldnt be able to set one in protected areas

work with the TRANSMAT ? ( teleport to inside the tardis )

 teleporting to an WayPoint , with a selection GUI