Those aren't mole hills, those are tree roots, but yeah, having cities permanently closed is just plain wrong. I bet they only did that because they couldn't fit any more data on the fourth disc. Or just didn't want to. At least they could do something like they did with Mideel in FFVII. It got destroyed, but you could still visit the people who were able to save themselves from getting engulfed into the Lifestreem.