explorationregions.gd only defines the pairs of dots connected by lines on the map.
In map.gd, the function "showtooltip(node)" creates the lines for each exit listed for the zone. The dots are Images displayed by TextureRect GUI controls(https://docs.godotengine.org/en/3.1/classes/class_texturerect.html). The position of those controls is what determines where the dot is. The name of those controls needs to match the name of a zone. The only way to get a zone to appear on the map is to add a new control node to the map.scn scene tree.
The following can be added to the beginning of _ready() in map.gd, as a minimal setup for adding a new red dot node:
var newNode = find_node("sea").duplicate()
newNode.rect_position = Vector2(100,100)
newNode.name = "newZone"
find_node("roads").add_child(newNode)