It's a little more complicated than that, because of how the "mega areas" in Secret are set up.
This was analysed by the UA hacking community a while ago (it's also not unique to Secret; at least some of the random encounter dungeons found near towns in Curse use this method, too). The mega areas (Old Verdigris, Mines, Ice Crevasses) are actually stored as one or more 16x16 dungeons on disk, and then automatic teleporter events are used to string pieces of them together into the dungeon layouts you actually experience (which explains the large amount of duplicate architecture seen especially in the ruins where the layout is denser - less so in the mines and crevasses as there are far fewer "active" cells so 256 Tetris'd together map cells goes further).
Coordinates are available in all such zones in Secret, but the area map *is not* (it would probably actually make things even more confusing as you'd likely see the crammed together layout instead of the actual relevant one!).
Anyway, I can see it being an issue for the map, because there is one effect of these automatic teleporters that I've seen, and that's that it's not 100% seamless - in particular, sometimes taking a step is silent and/or the coordinates do not update until you turn or move again, and if you're not paying careful attention to that I can see making mapping errors.