Sometimes it's important as admin to have a feature to give some permisson to some player or do something with waypoint.

For example if some player left a server and u want to change a waystone, the only way for you as an admin have to achieve that is to break the waypoint and place it again with your configuration. And if the player will return one day the waystone will be missing for them. Moreover all players will have to add this waypoint again after this process.
If some player put a waystone with a bad name I just want to rename it, not to break.
It looks like the case for the permisson system that exists since craftbukket and still used by the most admins.

The same goes and for /waystone commands. I can find myself in need to give a permission to someone to use a command. Or frobid from using it.