Right. given the usual nature of the game, I mark it down as an oversight that was just never addressed. To me, it would've made more sense for markers to be placed at better starting points for the hunt, such as at the entrance to the cave referenced in my above example, rather than on the exact horizontal spot of your goal and completely ignoring the vertical coordinates. It just made no sense at all.
The hunt for me was usually finding the entrance to the area the marker was in. Finding the actual object itself once I got into the place? That was easy, the marker was right on it.
It was only the overworld map that only gave the X and Y. Once you were nearby you could see that it was inside the ground and you had to look for an entrance.
I agree though, if its going to be an interior thing then the entrance better also have a marker so you know where to enter to head to the objective.