I have found with Waypoints, Zones and Checkpoints the stars that you use to define its area are always active and able to be moved, even when the object is locked.

This makes it hard when using these item indoors with other objects all around as you always seem to grab the stars instead of the item you are after.

It would be good to have the stars on these item locked as well so you cannot grab them by mistake.

Also it would be good to have a button on the toolbar in Top Down editor view to toggle the visibility of all of these items on / off, just because I find them distracting when modifying / building indoor areas, and then that way you wouldn't select them by mistake either.

maybe zones should be added into waypoint mode so you cant use those until you swap?

When you are in waypoint mode, waypoints are selectable and moveable of course, and entities are not selectable.

When you are in entity mode, waypoints are selectable and moveable and entities are selectable and moveable.

Maybe the Entity mode needs to be looked at to lock out the selection of the waypoints.