They worded that very badly, what they did was remove the portal so players can't get into the Pioneer's Coal Mine now. I guess that's better than it being useless.
As for their removing the function text from Nai and Mari, I'd have preferred they put puzzles and cubes on them like their function text said. What's the harm in having a puzzle/cube seller in Atlantis and Lilliput? Other versions have them there.