This works as long as the yellow xmarker is placed on valid navmesh, and the navmesh is finalized, which flags the triangle as having a door. The NPCs have to be able to navigate to the xmarker. The door itself can be out of reach.
The Location References are for things like a Boss, Map markers, load doors etc. Basically things that are very specific/important to a location. Just guessing, but I'd say they just copy as override the entire Location folder.