shouldnt there be some East/west/north/south waypoints to integrate the ufo in the routes of the other map blocks?
But nothing ever spawn in there.Is it perhaps because I'm using the LIGHTNIN tileset?
That would be my guess. If you check the LIGHTNING tileset with MCDEdit all tiles have byte 69 (special flag) defined as 1 = XCOM Craft. Try using a modded LIGHTNIN tileset with all the tiles having that byte defined as 0 to see what happens.