Nice to see you're able to play with the coordinates like that. I tried doing it with other games but since they weren't simple overhead games like RPGs, I couldn't find any manner of coordinates to work with.
As for the overworld, it's not surprising. The game developers wouldn't waste time finishing and polishing parts of a map that has no chance in hell of being seen. What you're talking about is probably either a tileset or just garbage data since there's nothing definite there.
I think the hard thing about mapping is balancing accuracy and aesthetism, and I've had to take hard decisions of this kind before.
For example, in my Zelda: Oracle Of Season overworld map, one screen had a tree tile that didn't fit with those of its neighboring screens, so I opted to correct it since it served to purpose to keep it accurate but looked better when changed.
On my Ufouria map which is comprised of several interconnecting sections like a Metroid map, all the sections fit together perfectly except one spot where there was the height of one tile between the floors of two sections (in short, by aligning all the other room transitions, I was throwing the last one out of alignment), so I actually added a single tile row to align everything, and nobody would notice while using the map unless they counted the number of tiles in the changed section.
So in short, I suggest to remove those tilesets unless they are of some significance (for example, in could be an in-joke and seen from far away, the tiles might form a message).
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"With the first link, the chain is forged. The first speech censored, the first thought forbidden, the first freedom denied, chains us all irrevocably." [...] The first time any man's freedom is trodden on, we're all damaged. - Captain Jean-Luc Picard
B*tch, meet reality. Reality, meet b*tch. - Me