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It seems the SKTileMapNode is using the most "in front" tile to decide the overlap logic for all other tiles of that same type. "In front" seems to mean down and left in your tile map node. For example, if you add a tile to the left-most tip of your map, that same tile copy will be in front of all other tile iterations.
A workaround (that is awful): Create copies in the tile set for all your tiles as many times as you need. You can use the same tile image, but it seems to be affecting the tile definition in your tile set. I'm filing a bug report with Feedback Assistant. Hopefully we get a fix...