Yah the map doesn't fit overall together but these maps do which is the point of mapping it and not route 1, you can see that the game just can't handle the original intention that is shown in the earlier concept art(since the game is only 4 directional):
As you see the wall is diagonal which is impossible in 4 Directions and the Power plant is on the top of the complete other side of the mountain, I wish it was possible to catch this amazing looking concept art completely but there are sadly limits to 4 directions when it comes to diagonal lines. This was less to have a world map and more of just the ones in the Rebuilt City, Azurine Lake and Apophyll that fit seamlessly for whatever reason people can use it, be that for the azurine lake navigation, just to enjoy seeing it fully or in my case to make high quality square pictures for the wiki pages. That is why the Beryl Ward Desert got extended up a bit on that side and why I just took and made the desert higher quality than is actually in the game.